rs9528775

Variant names:

• chr13-64504492-C-T
• rs9528775

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 0.499 in 151,642 control chromosomes in the GnomAD database, including 21,909 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 0.50 (21909 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 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: 0.499 AC: 75608 AN: 151524 Hom.: 21912 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.499 AC: 75605 AN: 151642 Hom.: 21909 Cov.: 31 AF XY: 0.499 AC XY: 36983 AN XY: 74058

African (AFR) AF: 0.201 AC: 8299 AN: 41312

American (AMR) AF: 0.457 AC: 6952 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2109 AN: 3464

East Asian (EAS) AF: 0.451 AC: 2310 AN: 5124

South Asian (SAS) AF: 0.530 AC: 2555 AN: 4818

European-Finnish (FIN) AF: 0.700 AC: 7367 AN: 10528

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44067 AN: 67880

Other (OTH) AF: 0.551 AC: 1161 AN: 2106

Alfa AF: 0.499 Hom.: 3211

Bravo AF: 0.468

Asia WGS AF: 0.436 AC: 1509 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.72
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs9528775; hg19: chr13-65078624;