Occurence |
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In All Control Samples | Select for variants that (do not) occur in any of the samples labeled as controls. Genotype specific filtering is available. |
Abs.Occ Control Samples | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your control samples. Occurence does not take quality filters into account for the control samples |
Rel.Occ Control Samples | Provide an relative value ( < 1 ) for the number of times a variant was seen in your control samples. Occurence does not take quality filters into account for the control samples |
Abs.Occ All Samples | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your samples. Occurence does not take quality filters into account for the cohort samples |
Rel.Occ All Samples | Provide an relative value ( < 1 ) for the number of times a variant was seen in your samples. Occurence does not take quality filters into account for the cohort samples |
Abs.Occ Female Samples | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your female samples. Occurence does not take quality filters into account for the female samples |
Rel.Occ Female Samples | Provide an relative value ( < 1 ) for the number of times a variant was seen in your female samples. Occurence does not take quality filters into account for the female samples |
Abs.Occ Male Samples | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your male samples. Occurence does not take quality filters into account for the male samples |
Rel.Occ Male Samples | Provide an relative value ( < 1 ) for the number of times a variant was seen in your male samples. Occurence does not take quality filters into account for the male samples |
In Selected Control Samples | DEPRECATED Select for variants that (do not) occur in a selection of the samples labeled as controls. Genotype specific filtering is available. |
Abs.Occ. Control Samples (Any Genotype) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your control samples. Occurence does not take quality filters into account for the control samples |
Abs.Occ. Control Samples (Heterozygous) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your control samples as a heterozygous call. Occurence does not take quality filters into account for the control samples. |
Abs.Occ. Control Samples (Homozygous Alt.) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your control samples as a homozygous call. Occurence does not take quality filters into account for the control samples. |
Rel.Occ. Control Samples (Any Genotype) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in. Occurence does not take quality filters into account for the control samples. |
Rel.Occ. Control Samples (Heterozygous) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in as a heterozygous call. Occurence does not take quality filters into account for the control samples. |
Rel.Occ. Control Samples (Homozygous Alt.) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in as a heterozygous call. Occurence does not take quality filters into account. |
Abs.Occ. All Samples (Any Genotype) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your samples. Occurence does not take quality filters into account |
Abs.Occ. All Samples (Heterozygous) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your samples as a heterozygous call. Occurence does not take quality filters into account |
Abs.Occ. All Samples (Homozygous Alt.) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in your samples as a homozygous call. Occurence does not take quality filters into account |
Rel.Occ. All Samples (Any Genotype) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in. Occurence does not take quality filters into account |
Rel.Occ. All Samples (Heterozygous) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in as a heterozygous call. Occurence does not take quality filters into account |
Rel.Occ. All Samples (Homozygous Alt.) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in as a homozygous call. Occurence does not take quality filters into account |
Abs.Occ. By Project (Any Genotype.All Samples) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in certain Projects. Occurence does not take quality filters into account |
Abs.Occ. By Project (Any Alternate.All Samples) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in certain Projects. Occurence does not take quality filters into account |
Abs.Occ. By Project (Any Genotype) | DEPRECATED Provide an absolute value ( >0 !! ) for the number of times a variant was seen in certain Project. Occurence does not take quality filters into account |
Abs.Occ. By Project (Homozygous Ref) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in certain Project as a homozygous reference call. This filter takes GVCF entries with GQ > 20 into account as reference calls. Occurence does not take quality filters into account |
Abs.Occ. By Project (Heterozygous) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in certain Project as a heterozygous call. Occurence does not take quality filters into account |
Abs.Occ. By Project (Homozygous Alt.) | Provide an absolute value ( >0 !! ) for the number of times a variant was seen in certain Project as a homozygous alternative call. Occurence does not take quality filters into account |
Rel.Occ. By Project (Any Genotype) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in a selection of projects. Occurence does not take quality filters into account |
Rel.Occ. By Project (Heterozygous) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in a selection of projects as a heterozygous call. Occurence does not take quality filters into account |
Rel.Occ. By Project (Homozygous Alt.) | Provide a fraction in the range of 0-1, of your samples that the variant was seen in a selection of projects as a heterozygous call. Occurence does not take quality filters into account |
Gene Hit In Other Cases (RefSeq VariantType) | Filter for variants affecting (RefSeq) genes, that are also affected by variants of the selected types in other cases you have access to. Other parameters such as quality are not taken into account for additional samples. Provide the minimal number of ADDITIONAL hits in the gene in the text field. Control samples are excluded as additional hits |
Gene Hit In Other Cases (RefGene VariantType) | Filter for variants affecting (RefGene) genes, that are also affected by variants of the selected types in other cases you have access to. Other parameters such as quality are not taken into account for additional samples. Provide the minimal number of ADDITIONAL hits in the gene in the text field. Control samples are excluded as additional hits |
Gene Hit In Other Cases (SnpEff Impact) | Filter for variants affecting (Ensembl) genes, that are also affected by variants of the selected SnpEff Impact types in other cases you have access to. Other parameters such as quality are not taken into account for additional samples. Provide the minimal number of ADDITIONAL hits in the gene in the text field. Control samples are excluded as additional hits |
In dbSNP v130 | DEPRECATED Include/Exclude all variants present in dbSNP v130 |
In dbSNP v135 | DEPRECATED Include/Exclude all variants present in dbSNP v135 |
dbSNP v135 MAF | DEPRECATED Include/Exclude variants present in dbSNPv135 based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In dbSNP v137 | DEPRECATED Include/Exclude all variants present in dbSNP v137 |
dbSNP v137 MAF | DEPRECATED Include/Exclude variants present in dbSNPv137 based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In dbSNP v138 | Include/Exclude all variants present in dbSNP v138 |
dbSNP v138 MAF | Include/Exclude variants present in dbSNPv138 based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In dbSNP v142 | Include/Exclude all variants present in dbSNP v142 |
dbSNP v142 MAF | Include/Exclude variants present in dbSNPv142 based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
dbSNP v142 nrChr | Include/Exclude variants present in dbSNPv142 based on a population size (number of chromosomes). Note: Variants not listed in dbSNP have a chormosome count of zero. |
In gnomAD g 2.1 | Include/Exclude all variants present in the gnomAD v2.1 genome samples. |
gnomAD g 2.1 AF (ALL) | Include/Exclude variants present in the gnomAD v2.1 genome samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (ALL) | Include/Exclude variants present in the gnomAD v2.1 genome samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (ALL) | Include/Exclude variants present in the gnomAD v2.1 genome samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (NFE) | Include/Exclude variants present in the gnomAD v2.1 genome NFE samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (NFE) | Include/Exclude variants present in the gnomAD v2.1 genome NFE samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (NFE) | Include/Exclude variants present in the gnomAD v2.1 genome NFE samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (Controls) | Include/Exclude variants present in the gnomAD v2.1 genome control samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (Controls) | Include/Exclude variants present in the gnomAD v2.1 genome control samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (Controls) | Include/Exclude variants present in the gnomAD v2.1 genome control samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (Female Controls) | Include/Exclude variants present in the gnomAD v2.1 genome female control samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (Female Controls) | Include/Exclude variants present in the gnomAD v2.1 genome female control samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (Female Controls) | Include/Exclude variants present in the gnomAD v2.1 genome female control samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (Male Controls) | Include/Exclude variants present in the gnomAD v2.1 genome male control samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (Male Controls) | Include/Exclude variants present in the gnomAD v2.1 genome male control samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (Male Controls) | Include/Exclude variants present in the gnomAD v2.1 genome male control samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (NFE Controls) | Include/Exclude variants present in the gnomAD v2.1 genome NFE control samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (NFE Controls) | Include/Exclude variants present in the gnomAD v2.1 genome NFE control samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (NFE Controls) | Include/Exclude variants present in the gnomAD v2.1 genome NFE control samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome non_topmed samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome non_topmed samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome non_topmed samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (Female non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome female non_topmed samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (Female non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome female non_topmed samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (Female non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome female non_topmed samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (Male non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome male non_topmed samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (Male non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome male non_topmed samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (Male non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome male non_topmed samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (NFE non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome NFE non_topmed samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (NFE non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome NFE non_topmed samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (NFE non topmed) | Include/Exclude variants present in the gnomAD v2.1 genome NFE non_topmed samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome non_neuro samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome non_neuro samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome non_neuro samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (Female non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome female non_neuro samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (Female non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome female non_neuro samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (Female non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome female non_neuro samples based on amount of homozygous samples. |
gnomAD g 2.1 AF (Male non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome male non_neuro samples based on a allele frequency. might be ambiguous for multi-allelic snps! |
gnomAD g 2.1 AN (Male non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome male non_neuro samples based on amount of covered alleles. |
gnomAD g 2.1 nHomAlt (Male non neuro) | Include/Exclude variants present in the gnomAD v2.1 genome male non_neuro samples based on amount of homozygous samples. |
In ESP5400 all | DEPRECATED Include/Exclude all variants present in the Exome Sequencing Project, release 5400, all populations |
ESP5400 all MAF | DEPRECATED Include/Exclude variants present in esp5400 all populations based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In ESP5400 ea | DEPRECATED Include/Exclude all variants present in the Exome Sequencing Project, release 5400, European Americans |
ESP5400 ea MAF | DEPRECATED Include/Exclude variants present in esp5400 ea population based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In ESP5400 aa | DEPRECATED Include/Exclude all variants present in the Exome Sequencing Project, release 5400, African Americans |
ESP5400 aa MAF | DEPRECATED Include/Exclude variants present in esp5400 aa population based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In ESP6500 all | Include/Exclude all variants present in the Exome Sequencing Project, release 6500, all populations |
ESP6500 all MAF | Include/Exclude variants present in esp6500 all populations based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In ESP6500 ea | Include/Exclude all variants present in the Exome Sequencing Project, release 6500, European Americans |
ESP6500 ea MAF | Provide a minor allele frequency. might be ambiguous for multi-allelic snps! |
In ESP6500 aa | Include/Exclude all variants present in the Exome Sequencing Project, release 6500, African Americans |
ESP6500 aa MAF | Provide a minor allele frequency. might be ambiguous for multi-allelic snps! |
In ExAC v02 | DEPRECATED Include/Exclude all variants present in the ExAC database, release 02, All populations |
ExAC v02 MAF | DEPRECATED Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR ALL_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
In ExAC v03 ALL | Include/Exclude all variants present in the ExAC database, release 03, All populations |
ExAC v03 MAF ALL | Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR ALL_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
ExAC v03 nrChr ALL | Provide a minimal number of chromosomes included for genotyping the variant in ALL populations |
In ExAC v03 AFR | Include/Exclude all variants present in the ExAC database, release 03, AFR population |
ExAC v03 MAF AFR | Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR AFR_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
ExAC v03 nrChr AFR | Provide a minimal number of chromosomes included for genotyping the variant in AFR population |
In ExAC v03 AMR | Include/Exclude all variants present in the ExAC database, release 03, AMR population |
ExAC v03 MAF AMR | Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR AMR_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
ExAC v03 nrChr AMR | Provide a minimal number of chromosomes included for genotyping the variant in AMR population |
In ExAC v03 EAS | Include/Exclude all variants present in the ExAC database, release 03, EAS population |
ExAC v03 MAF EAS | Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR EAS_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
ExAC v03 nrChr EAS | Provide a minimal number of chromosomes included for genotyping the variant in EAS population |
In ExAC v03 FIN | Include/Exclude all variants present in the ExAC database, release 03, FIN population |
ExAC v03 MAF FIN | Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR FIN_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
ExAC v03 nrChr FIN | Provide a minimal number of chromosomes included for genotyping the variant in FIN population |
In ExAC v03 NFE | Include/Exclude all variants present in the ExAC database, release 03, NFE population |
ExAC v03 MAF NFE | Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR NFE_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
ExAC v03 nrChr NFE | Provide a minimal number of chromosomes included for genotyping the variant in NFE population |
In ExAC v03 OTH | Include/Exclude all variants present in the ExAC database, release 03, OTH population |
ExAC v03 MAF OTH | Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR OTH_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
ExAC v03 nrChr OTH | Provide a minimal number of chromosomes included for genotyping the variant in OTH population |
In ExAC v03 SAS | Include/Exclude all variants present in the ExAC database, release 03, SAS population |
ExAC v03 MAF SAS | Provide a minor allele frequency. Although values are similar, there are discrepancies between ANNOVAR SAS_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20) |
ExAC v03 nrChr SAS | Provide a minimal number of chromosomes included for genotyping the variant in SAS population |
In Kaviar 150923 | Include/Exclude all variants present in the Kaviar database, release 20150923 |
Kaviar 150923 MAF | Provide a minor allele frequency for the Kaviar database, release 20150923 |
Kaviar 150923 nrChr | Provide a minimal number of chromosomes included for genotyping the variant Kaviar, release 20150923 |
In 1000g2012apr all | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, all populations |
1000g2012apr all MAF | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, all populations, based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In 1000g2012apr afr | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, afr population |
1000g2012apr afr MAF | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, afr population, based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In 1000g2012apr amr | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, amr population |
1000g2012apr amr MAF | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, amr population, based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In 1000g2012apr asn | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, asn population |
1000g2012apr asn MAF | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, asn population, based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
In 1000g2012apr eur | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, eur population |
1000g2012apr eur MAF | DEPRECATED Include/Exclude all variants present in the 1000 genomes project, release 2012-04, eur population, based on a minor allele frequency. might be ambiguous for multi-allelic snps! |
|
Mutation_Effect_Predictions |
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CADDv1.4 Phred | CADD v1.4 Phred-Scores. Integrated pathogenicity predication score, see publication for details (pmid: 24487276). The scores represent the likelyhood that the variant is pathogenic, as being in the top (10 to the power minus the Score)th percent of genome wide variants. |
dbSNP v135 Clinical | DEPRECATED Select Variants from dbSNPv135 that are tagged as clinically relevant. This is a recent feature and contains many unclear entries |
dbSNP v137 Clinical | DEPRECATED Select Variants from dbSNPv137 that are tagged as clinically relevant. This is a recent feature and contains many unclear entries |
dbSNP v138 Clinical | Select Variants from dbSNPv138 that are tagged as clinically relevant. This is a recent feature and contains many unclear entries |
LJB GERP Score | DEPRECATED GERP is a conservation score. High score is indicative of constrained site. (See Davidov et al, 2010, plos computational biology) |
LJB LRT Score | DEPRECATED Rescaled (0-1) likelihood ratio test of codon constrained. Higher score for more constrained codons. See dbNSFP paper for details (pmid: 21520341) |
LJB Mutation Taster Score | DEPRECATED Mutation Taster has four categories: (A)utomatic and (D)isease causing, for which the score is p-value for a true prediction. (N)on-deleterious and (P)olymorphism known, for which the score is 1 - p-value for a true prediction. The higher the score, the more likely the variant is deleterious. See dbNSFP paper for details (pmid: 21520341) |
LJB PhyloP Score | DEPRECATED Rescaled (0-1) PhyloP score. Higher Score for more conserved sites. Prediction is Rescaled Score higher than 0.95 for a conserved site. See dbNSFP paper for details (pmid: 21520341). Note: Vissers et al reported PhyloP threshold of 2.5, rescaled to 0.998 for deleterious variants. |
LJB PolyPhen2 Score | DEPRECATED Polyphen2 score. Higher Score for more likely damaging sites. Prediction is probably damaging if higher than 0.85 for a damaging site. Possibly damaging between 0.85 and 0.15. See dbNSFP paper for details (pmid: 21520341). |
LJB Sift Score | DEPRECATED Rescaled Sift score. Higher Score for more likely damaging sites. Prediction is damaging if higher than 0.95. See dbNSFP paper for details (pmid: 21520341). |
CADD Raw Score | DEPRECATED CADD C-Scores. Integrated pathogenicity predication score. Raw Scores, see publication for details (pmid: 24487276). |
CADD Phred Score | DEPRECATED CADD C-Scores in Phred Scale. E.g.: Scores above 20 are in the 1% top scoring variants, scores above 30 are in the 0.1% top scoring variants (pmid: 24487276). |
WebTool Sift Score | Rescaled Sift score. Higher Score for more likely damaging sites. Prediction is damaging if higher than 0.95. Scores are obtained from the PROVEAN WebTool. |
WebTool PROVEAN Score | PROVEAN score. Score below -2.5 indicates likely damaging sites. Scores are obtained from the PROVEAN WebTool. |
WebTool Grantham Score | PROVEAN score. Score below -2.5 indicates likely damaging sites. Scores are obtained from the PROVEAN WebTool. |
WebTool MutationTaster Score | Mutation Taster has four categories: (A)utomatic and (D)isease causing, for which the score is p-value for a true prediction. (N)on-deleterious and (P)olymorphism known, for which the score is 1 - p-value for a true prediction. The higher the score, the more likely the variant is deleterious. High score for class P, might indicate a false positive in reference databases such as dbSNP. Scores are obtained from the MTQE. |
dbnsfp30a SIFT Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with lower values being more likely to represent pathogenicity. The proposed threshold for SIFT is 0.05 |
dbnsfp30a pph2 HDIV Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The proposed threshold for PolyPhen2_HDIV is 0.5 (Neutral vs non-neutral), or 0.957 and 0.453 (Probably damaging, possibly damaging, neutral) |
dbnsfp30a pph2 HVAR Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The proposed threshold for PolyPhen2_HVAR is 0.5 (Neutral vs non-neutral), or 0.909 and 0.447 (Probably damaging, possibly damaging, neutral) |
dbnsfp30a LRT pred | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The Likelyhood ratio test is a composite descision logic, providing benign,damaging or unclear classes |
dbnsfp30a MutationTaster Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The proposed threshold for MutationTaster is 0.5 |
dbnsfp30a MutationAssessor Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between -5.545 and 5.975, with higher values being more likely to represent pathogenicity. The proposed threshold for MutationAssessor is 0.65 |
dbnsfp30a FATHMM Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between -16.13 and 10.64, with smaller values being more likely to represent pathogenicity. The proposed threshold for FATHMM is -1.5 |
dbnsfp30a FATHMM MKL Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The proposed threshold for FATHMM_MKL_coding is 0.5 |
dbnsfp30a PROVEAN Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between -14 and 14, with smaller values being more likely to represent pathogenicity. The proposed threshold for PROVEAN is -2.5 |
dbnsfp30a VEST3 Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The proposed threshold for VEST3 is not provided |
dbnsfp30a CADD Phred | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. CADD_phred scores should be interpreted as being in the 10^score % of most pathogenic variants. NOTE: dbNSFP only provides scores for EXONIC SNVs! |
dbnsfp30a DANN Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The proposed threshold for DANN is not provided |
dbnsfp30a MetaSVM Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between -2 and 3, with higher values being more likely to represent pathogenicity. The proposed threshold for MetaSVM is 0 |
dbnsfp30a MetaLR Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The proposed threshold for MetaLR is 0.5 |
dbnsfp30a Integrated fitCons Score | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between 0 and 1, with higher values being more likely to represent pathogenicity. The proposed threshold for fitCons is not provided |
dbnsfp30a GERP RS | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Prediction are between -12.3 and 6.17. Higher values more likely represent pathogenicity. The proposed threshold for GERP is 4.4 |
dbnsfp30a PhyloP7 vert | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions are between -5.172 and 1.062. Higher values more likely represent pathogenicity. The proposed threshold for PhyloP is not provided |
dbnsfp30a PhyloP20 mam | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions range between -13.282 and 1.199. Higher values more likely represent pathogenicity. The proposed threshold for PhyloP is not provided |
dbnsfp30a SiPhy 29way | dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Predictions range between 0 and 37.9718. Higher values more likely represent pathogenicity. The proposed threshold for SiPhy is not provided |
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