rs1961397

Variant names:

• chr3-187911139-A-G
• rs1961397

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 0.154 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0813

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.153

Alfa AF: 0.111 Hom.: 655

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

Splicing

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

Publications

LitVar

Other links and lift over

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