rs731908

chr13-102915313-C-Achr13-102915313-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.188 in 152,164 control chromosomes in the GnomAD database, including 3,457 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 0.19 (3457 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 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: 0.188 AC: 28570 AN: 152046 Hom.: 3451 Cov.: 33

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.188 AC: 28585 AN: 152164 Hom.: 3457 Cov.: 33 AF XY: 0.190 AC XY: 14159 AN XY: 74396

Gnomad4 AFR AF: 0.0882

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.199

Alfa AF: 0.194 Hom.: 4322

Bravo AF: 0.193

Asia WGS AF: 0.418 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	19
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs731908; hg19: chr13-103567663;