rs13290443

Variant names:

• chr9-130153008-T-C
• rs13290443

Your query was ambiguous. Multiple possible variants found:

• chr9-130153008-T-C
• chr9-130153008-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 0.498 in 151,642 control chromosomes in the GnomAD database, including 19,492 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 0.50 (19492 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 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: 0.498 AC: 75425 AN: 151524 Hom.: 19476 Cov.: 29

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.498 AC: 75476 AN: 151642 Hom.: 19492 Cov.: 29 AF XY: 0.494 AC XY: 36644 AN XY: 74124

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.503

Alfa AF: 0.547 Hom.: 25962

Bravo AF: 0.485

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13290443; hg19: chr9-132915287; COSMIC: COSV60403183;