chr3-161764857-G-T

Variant names:

• chr3-161764857-G-T
• rs308690

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 0.404 in 151,538 control chromosomes in the GnomAD database, including 12,609 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 0.40 (12609 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 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: 0.404 AC: 61135 AN: 151418 Hom.: 12602 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.404 AC: 61173 AN: 151538 Hom.: 12609 Cov.: 31 AF XY: 0.404 AC XY: 29892 AN XY: 74028

African (AFR) AF: 0.320 AC: 13226 AN: 41390

American (AMR) AF: 0.471 AC: 7161 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1687 AN: 3468

East Asian (EAS) AF: 0.274 AC: 1400 AN: 5114

South Asian (SAS) AF: 0.496 AC: 2378 AN: 4796

European-Finnish (FIN) AF: 0.361 AC: 3804 AN: 10526

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 29960 AN: 67738

Other (OTH) AF: 0.432 AC: 906 AN: 2098

Alfa AF: 0.429 Hom.: 55701

Bravo AF: 0.404

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.1
DANN	Benign	0.48
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs308690; hg19: chr3-161482645; COSMIC: COSV69625245;