rs731908

Variant names:

• chr13-102915313-C-A
• rs731908

Your query was ambiguous. Multiple possible variants found:

• chr13-102915313-C-A
• chr13-102915313-C-G
• chr13-102915313-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0882 AC: 3662 AN: 41508

American (AMR) AF: 0.255 AC: 3898 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 806 AN: 3466

East Asian (EAS) AF: 0.539 AC: 2786 AN: 5172

South Asian (SAS) AF: 0.359 AC: 1731 AN: 4824

European-Finnish (FIN) AF: 0.181 AC: 1915 AN: 10578

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13185 AN: 68010

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.195 Hom.: 9888

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs731908; hg19: chr13-103567663;