rs6131295

Variant names:

• chr20-12015619-G-A
• rs6131295

Your query was ambiguous. Multiple possible variants found:

• chr20-12015619-G-A
• chr20-12015619-G-C
• chr20-12015619-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.79 in 150,020 control chromosomes in the GnomAD database, including 47,047 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (47047 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.790 AC: 118394 AN: 149916 Hom.: 46996 Cov.: 26

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.811

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.794

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.790 AC: 118498 AN: 150020 Hom.: 47047 Cov.: 26 AF XY: 0.792 AC XY: 57841 AN XY: 73060

African (AFR) AF: 0.849 AC: 34423 AN: 40532

American (AMR) AF: 0.828 AC: 12492 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2849 AN: 3464

East Asian (EAS) AF: 0.777 AC: 3939 AN: 5072

South Asian (SAS) AF: 0.773 AC: 3669 AN: 4748

European-Finnish (FIN) AF: 0.784 AC: 7872 AN: 10036

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50631 AN: 67806

Other (OTH) AF: 0.795 AC: 1656 AN: 2082

Alfa AF: 0.762 Hom.: 186857

Bravo AF: 0.800

Asia WGS AF: 0.798 AC: 2776 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.22
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6131295; hg19: chr20-11996267;