chr3-128477657-G-A

Variant names:

• chr3-128477657-G-A
• rs2713594

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 0.472 in 152,010 control chromosomes in the GnomAD database, including 17,395 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 0.47 (17395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.472 AC: 71626 AN: 151892 Hom.: 17373 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.472 AC: 71697 AN: 152010 Hom.: 17395 Cov.: 32 AF XY: 0.472 AC XY: 35028 AN XY: 74284

African (AFR) AF: 0.540 AC: 22381 AN: 41428

American (AMR) AF: 0.488 AC: 7457 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1751 AN: 3460

East Asian (EAS) AF: 0.550 AC: 2837 AN: 5162

South Asian (SAS) AF: 0.539 AC: 2595 AN: 4816

European-Finnish (FIN) AF: 0.402 AC: 4249 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28809 AN: 67972

Other (OTH) AF: 0.464 AC: 980 AN: 2110

Alfa AF: 0.442 Hom.: 48996

Bravo AF: 0.480

Asia WGS AF: 0.510 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.87
DANN	Benign	0.43
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2713594; hg19: chr3-128196500;