rs9525562

Variant names:

• chr13-42037531-C-A
• rs9525562

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 0.342 in 152,000 control chromosomes in the GnomAD database, including 9,005 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 0.34 (9005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 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: 0.342 AC: 51924 AN: 151882 Hom.: 8986 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.342 AC: 51974 AN: 152000 Hom.: 9005 Cov.: 32 AF XY: 0.339 AC XY: 25204 AN XY: 74324

African (AFR) AF: 0.343 AC: 14218 AN: 41440

American (AMR) AF: 0.232 AC: 3546 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3466

East Asian (EAS) AF: 0.347 AC: 1793 AN: 5164

South Asian (SAS) AF: 0.323 AC: 1553 AN: 4810

European-Finnish (FIN) AF: 0.374 AC: 3959 AN: 10572

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.359 AC: 24411 AN: 67960

Other (OTH) AF: 0.354 AC: 747 AN: 2108

Alfa AF: 0.348 Hom.: 2731

Bravo AF: 0.333

Asia WGS AF: 0.405 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.15
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs9525562; hg19: chr13-42611667;