3-142904956-T-A

Variant names:

• chr3-142904956-T-A
• rs1479137

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 0.385 in 152,046 control chromosomes in the GnomAD database, including 13,420 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 0.39 (13420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 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: 0.386 AC: 58577 AN: 151926 Hom.: 13419 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.385 AC: 58585 AN: 152046 Hom.: 13420 Cov.: 32 AF XY: 0.389 AC XY: 28864 AN XY: 74282

African (AFR) AF: 0.148 AC: 6124 AN: 41490

American (AMR) AF: 0.341 AC: 5208 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1860 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1328 AN: 5172

South Asian (SAS) AF: 0.313 AC: 1505 AN: 4806

European-Finnish (FIN) AF: 0.610 AC: 6443 AN: 10556

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34620 AN: 67962

Other (OTH) AF: 0.386 AC: 811 AN: 2100

Alfa AF: 0.322 Hom.: 988

Bravo AF: 0.359

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1479137; hg19: chr3-142623798;