rs2157081

Variant names:

• chr6-32793999-G-A
• rs2157081

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 0.673 in 152,062 control chromosomes in the GnomAD database, including 34,693 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 0.67 (34693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.787 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: 0.674 AC: 102340 AN: 151944 Hom.: 34683 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.673 AC: 102387 AN: 152062 Hom.: 34693 Cov.: 31 AF XY: 0.680 AC XY: 50569 AN XY: 74342

African (AFR) AF: 0.652 AC: 27032 AN: 41458

American (AMR) AF: 0.657 AC: 10035 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2459 AN: 3468

East Asian (EAS) AF: 0.719 AC: 3717 AN: 5170

South Asian (SAS) AF: 0.808 AC: 3901 AN: 4826

European-Finnish (FIN) AF: 0.769 AC: 8138 AN: 10576

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44680 AN: 67968

Other (OTH) AF: 0.685 AC: 1445 AN: 2110

Alfa AF: 0.663 Hom.: 33864

Bravo AF: 0.659

Asia WGS AF: 0.750 AC: 2609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.59
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2157081; hg19: chr6-32761776;