rs1961397

Positions:

• chr3-187911139-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;