3-137967114-T-C

Variant names:

• chr3-137967114-T-C
• rs7632392

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 0.663 in 151,744 control chromosomes in the GnomAD database, including 34,883 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 0.66 (34883 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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: 0.663 AC: 100556 AN: 151626 Hom.: 34868 Cov.: 30

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.663 AC: 100614 AN: 151744 Hom.: 34883 Cov.: 30 AF XY: 0.666 AC XY: 49338 AN XY: 74126

African (AFR) AF: 0.443 AC: 18342 AN: 41364

American (AMR) AF: 0.658 AC: 9997 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3470

East Asian (EAS) AF: 0.697 AC: 3599 AN: 5164

South Asian (SAS) AF: 0.760 AC: 3654 AN: 4810

European-Finnish (FIN) AF: 0.783 AC: 8215 AN: 10488

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51945 AN: 67948

Other (OTH) AF: 0.687 AC: 1445 AN: 2102

Alfa AF: 0.739 Hom.: 26647

Bravo AF: 0.643

Asia WGS AF: 0.719 AC: 2498 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.32
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7632392; hg19: chr3-137685956;