rs769592

Variant names:

• chr3-192929974-C-A
• rs769592

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 0.451 in 151,882 control chromosomes in the GnomAD database, including 15,551 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 0.45 (15551 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.522 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: 0.451 AC: 68459 AN: 151764 Hom.: 15522 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.451 AC: 68529 AN: 151882 Hom.: 15551 Cov.: 31 AF XY: 0.453 AC XY: 33640 AN XY: 74230

African (AFR) AF: 0.419 AC: 17330 AN: 41398

American (AMR) AF: 0.532 AC: 8108 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1851 AN: 5156

South Asian (SAS) AF: 0.518 AC: 2499 AN: 4824

European-Finnish (FIN) AF: 0.455 AC: 4788 AN: 10524

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30658 AN: 67954

Other (OTH) AF: 0.470 AC: 989 AN: 2106

Alfa AF: 0.457 Hom.: 43299

Bravo AF: 0.460

Asia WGS AF: 0.453 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs769592; hg19: chr3-192647763;