rs779293

chr3-191877816-G-Achr3-191877816-G-Cchr3-191877816-G-T

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 0.332 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.346

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.6
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

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