rs951937

Variant names:

• chr3-162109746-T-A
• rs951937

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 0.162 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0405

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.00755

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.143

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951937; hg19: chr3-161827534;