3-157059338-T-C

Variant names:

• chr3-157059338-T-C
• rs2046273

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 0.622 in 152,062 control chromosomes in the GnomAD database, including 31,712 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 0.62 (31712 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.622 AC: 94537 AN: 151944 Hom.: 31698 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.622 AC: 94578 AN: 152062 Hom.: 31712 Cov.: 32 AF XY: 0.632 AC XY: 47019 AN XY: 74342

African (AFR) AF: 0.349 AC: 14502 AN: 41500

American (AMR) AF: 0.725 AC: 11061 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2373 AN: 3466

East Asian (EAS) AF: 0.831 AC: 4297 AN: 5172

South Asian (SAS) AF: 0.823 AC: 3962 AN: 4816

European-Finnish (FIN) AF: 0.754 AC: 7971 AN: 10578

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48177 AN: 67952

Other (OTH) AF: 0.630 AC: 1326 AN: 2106

Alfa AF: 0.686 Hom.: 16816

Bravo AF: 0.607

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs2046273; hg19: chr3-156777127;