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. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.425 AC: 17593 AN: 41352

American (AMR) AF: 0.488 AC: 7432 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3468

East Asian (EAS) AF: 0.118 AC: 603 AN: 5094

South Asian (SAS) AF: 0.442 AC: 2119 AN: 4792

European-Finnish (FIN) AF: 0.567 AC: 5974 AN: 10528

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38186 AN: 67864

Other (OTH) AF: 0.503 AC: 1060 AN: 2108

Alfa AF: 0.542 Hom.: 33297

Bravo AF: 0.485

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		0.18

Splicing

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

Other links and lift over

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