rs9533425

Variant names:

• chr13-43196338-G-C
• rs9533425

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 0.134 in 152,198 control chromosomes in the GnomAD database, including 1,818 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 0.13 (1818 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.134 AC: 20454 AN: 152080 Hom.: 1817 Cov.: 32

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.134 AC: 20455 AN: 152198 Hom.: 1818 Cov.: 32 AF XY: 0.132 AC XY: 9810 AN XY: 74416

Gnomad4 AFR AF: 0.0347

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.140

Alfa AF: 0.164 Hom.: 294

Bravo AF: 0.125

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9533425; hg19: chr13-43770474;