chr3-191877816-G-A

Variant names:

• chr3-191877816-G-A
• rs779293

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 0.332 in 151,864 control chromosomes in the GnomAD database, including 9,751 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 0.33 (9751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50408 AN: 151748 Hom.: 9743 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.332 AC: 50423 AN: 151864 Hom.: 9751 Cov.: 32 AF XY: 0.337 AC XY: 25005 AN XY: 74182

African (AFR) AF: 0.122 AC: 5059 AN: 41414

American (AMR) AF: 0.354 AC: 5400 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1988 AN: 5160

South Asian (SAS) AF: 0.420 AC: 2019 AN: 4812

European-Finnish (FIN) AF: 0.466 AC: 4909 AN: 10528

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.417 AC: 28315 AN: 67928

Other (OTH) AF: 0.346 AC: 730 AN: 2108

Alfa AF: 0.251 Hom.: 680

Bravo AF: 0.311

Asia WGS AF: 0.395 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs779293; hg19: chr3-191595605; COSMIC: COSV68404210;