3-1596929-A-G

Variant names:

• chr3-1596929-A-G
• rs6779648

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.509 in 151,566 control chromosomes in the GnomAD database, including 21,131 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 0.51 (21131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77139 AN: 151446 Hom.: 21130 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.509 AC: 77164 AN: 151566 Hom.: 21131 Cov.: 32 AF XY: 0.511 AC XY: 37821 AN XY: 74030

African (AFR) AF: 0.289 AC: 11977 AN: 41420

American (AMR) AF: 0.525 AC: 7975 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1957 AN: 3460

East Asian (EAS) AF: 0.581 AC: 2978 AN: 5124

South Asian (SAS) AF: 0.695 AC: 3340 AN: 4806

European-Finnish (FIN) AF: 0.556 AC: 5824 AN: 10472

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41196 AN: 67780

Other (OTH) AF: 0.528 AC: 1112 AN: 2108

Alfa AF: 0.565 Hom.: 44916

Bravo AF: 0.493

Asia WGS AF: 0.573 AC: 1988 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	19
DANN	Benign	0.89
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6779648; hg19: chr3-1638613;