rs9318942

Variant names:

• chr13-83456379-T-C
• rs9318942

Your query was ambiguous. Multiple possible variants found:

• chr13-83456379-T-C
• chr13-83456379-T-G

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 0.762 in 151,950 control chromosomes in the GnomAD database, including 45,795 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 0.76 (45795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 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: 0.762 AC: 115627 AN: 151832 Hom.: 45766 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.762 AC: 115714 AN: 151950 Hom.: 45795 Cov.: 32 AF XY: 0.759 AC XY: 56351 AN XY: 74264

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.778

Alfa AF: 0.855 Hom.: 30078

Bravo AF: 0.740

Asia WGS AF: 0.632 AC: 2196 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9318942; hg19: chr13-84030514;