rs9533425

Variant names:

• chr13-43196338-G-C
• rs9533425

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 0.134 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0347 AC: 1442 AN: 41546

American (AMR) AF: 0.106 AC: 1626 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3464

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5176

South Asian (SAS) AF: 0.108 AC: 520 AN: 4814

European-Finnish (FIN) AF: 0.185 AC: 1956 AN: 10590

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13839 AN: 67998

Other (OTH) AF: 0.140 AC: 295 AN: 2114

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs9533425; hg19: chr13-43770474;