rs13290443

chr9-130153008-T-Cchr9-130153008-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/exons	MANE	UniProt

Ensembl

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