rs13269433

Variant names:

• chr8-8596652-C-T
• rs13269433

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 0.123 in 151,216 control chromosomes in the GnomAD database, including 1,571 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 (1571 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 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: 0.123 AC: 18574 AN: 151106 Hom.: 1572 Cov.: 27

Gnomad AFR AF: 0.0337

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.00136

Gnomad SAS AF: 0.0829

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.123 AC: 18560 AN: 151216 Hom.: 1571 Cov.: 27 AF XY: 0.117 AC XY: 8619 AN XY: 73820

Gnomad4 AFR AF: 0.0336

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.00137

Gnomad4 SAS AF: 0.0818

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.140

Alfa AF: 0.141 Hom.: 288

Bravo AF: 0.123

Asia WGS AF: 0.0400 AC: 142 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13269433; hg19: chr8-8454162;