3-137937756-C-A

Variant names:

• chr3-137937756-C-A
• rs1429759

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 0.523 in 151,952 control chromosomes in the GnomAD database, including 23,246 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 0.52 (23246 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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: 0.523 AC: 79453 AN: 151832 Hom.: 23240 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.523 AC: 79478 AN: 151952 Hom.: 23246 Cov.: 31 AF XY: 0.527 AC XY: 39111 AN XY: 74254

African (AFR) AF: 0.229 AC: 9474 AN: 41440

American (AMR) AF: 0.571 AC: 8710 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2210 AN: 3466

East Asian (EAS) AF: 0.690 AC: 3563 AN: 5162

South Asian (SAS) AF: 0.626 AC: 3018 AN: 4818

European-Finnish (FIN) AF: 0.671 AC: 7086 AN: 10560

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43588 AN: 67928

Other (OTH) AF: 0.570 AC: 1205 AN: 2114

Alfa AF: 0.448 Hom.: 1579

Bravo AF: 0.503

Asia WGS AF: 0.642 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1429759; hg19: chr3-137656598;