rs951937

Variant names:

• chr3-162109746-T-A
• rs951937

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 0.162 in 152,058 control chromosomes in the GnomAD database, including 2,687 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 0.16 (2687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.162 AC: 24596 AN: 151938 Hom.: 2687 Cov.: 32

Gnomad AFR AF: 0.0406

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.00734

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.162 AC: 24597 AN: 152058 Hom.: 2687 Cov.: 32 AF XY: 0.161 AC XY: 11947 AN XY: 74292

African (AFR) AF: 0.0405 AC: 1682 AN: 41536

American (AMR) AF: 0.113 AC: 1729 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 505 AN: 3472

East Asian (EAS) AF: 0.00755 AC: 39 AN: 5166

South Asian (SAS) AF: 0.154 AC: 745 AN: 4826

European-Finnish (FIN) AF: 0.296 AC: 3122 AN: 10538

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16191 AN: 67946

Other (OTH) AF: 0.143 AC: 301 AN: 2108

Alfa AF: 0.206 Hom.: 485

Bravo AF: 0.141

Asia WGS AF: 0.0720 AC: 252 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs951937; hg19: chr3-161827534;