rs1961397

Variant names:

• chr3-187911139-A-G
• rs1961397

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 0.154 in 152,144 control chromosomes in the GnomAD database, including 2,399 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 0.15 (2399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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: 0.154 AC: 23396 AN: 152026 Hom.: 2396 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0813

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.154 AC: 23438 AN: 152144 Hom.: 2399 Cov.: 32 AF XY: 0.152 AC XY: 11309 AN XY: 74404

African (AFR) AF: 0.272 AC: 11275 AN: 41468

American (AMR) AF: 0.224 AC: 3417 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3470

East Asian (EAS) AF: 0.0813 AC: 421 AN: 5178

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4826

European-Finnish (FIN) AF: 0.0793 AC: 842 AN: 10620

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0975 AC: 6627 AN: 67986

Other (OTH) AF: 0.153 AC: 321 AN: 2104

Alfa AF: 0.112 Hom.: 726

Bravo AF: 0.173

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.77
DANN	Benign	0.77
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs1961397; hg19: chr3-187628927; COSMIC: COSV70964016;