rs9532969

Variant names:

• chr13-42017703-C-T
• rs9532969

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 0.303 in 152,122 control chromosomes in the GnomAD database, including 7,386 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 0.30 (7386 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 2 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 = 0.349 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: 0.303 AC: 46107 AN: 152004 Hom.: 7383 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.303 AC: 46114 AN: 152122 Hom.: 7386 Cov.: 33 AF XY: 0.303 AC XY: 22532 AN XY: 74390

African (AFR) AF: 0.210 AC: 8692 AN: 41486

American (AMR) AF: 0.234 AC: 3570 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1802 AN: 5170

South Asian (SAS) AF: 0.334 AC: 1614 AN: 4826

European-Finnish (FIN) AF: 0.374 AC: 3964 AN: 10586

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 24011 AN: 67974

Other (OTH) AF: 0.341 AC: 720 AN: 2114

Alfa AF: 0.328 Hom.: 2459

Bravo AF: 0.292

Asia WGS AF: 0.391 AC: 1357 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	2.2
DANN	Benign	0.69
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs9532969; hg19: chr13-42591839;