rs9634941

Positions:

• chr13-68474117-G-A

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/exons	MANE	UniProt

Ensembl

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