rs9634941

Variant names:

• chr13-68474117-G-A
• rs9634941

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 0.116 in 151,680 control chromosomes in the GnomAD database, including 1,125 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 0.12 (1125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.865

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 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: 0.116 AC: 17590 AN: 151562 Hom.: 1122 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.116 AC: 17626 AN: 151680 Hom.: 1125 Cov.: 32 AF XY: 0.118 AC XY: 8766 AN XY: 74118

Gnomad4 AFR AF: 0.0882

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.0750

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.134

Alfa AF: 0.108 Hom.: 119

Bravo AF: 0.123

Asia WGS AF: 0.180 AC: 623 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9634941; hg19: chr13-69048249;