rs7632392

chr3-137967114-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.687

Alfa AF: 0.741 Hom.: 24428

Bravo AF: 0.643

Asia WGS AF: 0.719 AC: 2498 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.16
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7632392; hg19: chr3-137685956;