rs3117915

Variant names:

• chr13-22031441-A-G
• rs3117915

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 0.353 in 151,958 control chromosomes in the GnomAD database, including 11,488 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 0.35 (11488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.353 AC: 53636 AN: 151840 Hom.: 11470 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.353 AC: 53713 AN: 151958 Hom.: 11488 Cov.: 32 AF XY: 0.353 AC XY: 26199 AN XY: 74276

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.339

Alfa AF: 0.256 Hom.: 11248

Bravo AF: 0.372

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117915; hg19: chr13-22605580;