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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.795

Alfa AF: 0.758 Hom.: 86749

Bravo AF: 0.800

Asia WGS AF: 0.798 AC: 2776 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6131295; hg19: chr20-11996267;