3-176203096-G-T

Variant names:

• chr3-176203096-G-T
• rs4894505

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 0.627 in 152,014 control chromosomes in the GnomAD database, including 30,252 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 0.63 (30252 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95273 AN: 151896 Hom.: 30233 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.627 AC: 95349 AN: 152014 Hom.: 30252 Cov.: 32 AF XY: 0.626 AC XY: 46522 AN XY: 74316

African (AFR) AF: 0.575 AC: 23814 AN: 41426

American (AMR) AF: 0.624 AC: 9545 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2958 AN: 5164

South Asian (SAS) AF: 0.416 AC: 2009 AN: 4826

European-Finnish (FIN) AF: 0.715 AC: 7550 AN: 10556

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.670 AC: 45557 AN: 67966

Other (OTH) AF: 0.611 AC: 1292 AN: 2116

Alfa AF: 0.640 Hom.: 59492

Bravo AF: 0.620

Asia WGS AF: 0.523 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.6
DANN	Benign	0.43
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs4894505; hg19: chr3-175920884;