13-52920559-G-A

Variant names:

• chr13-52920559-G-A
• rs9536318

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 0.811 in 150,950 control chromosomes in the GnomAD database, including 49,764 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 0.81 (49764 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 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: 0.811 AC: 122326 AN: 150832 Hom.: 49734 Cov.: 27

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.811 AC: 122404 AN: 150950 Hom.: 49764 Cov.: 27 AF XY: 0.810 AC XY: 59626 AN XY: 73616

African (AFR) AF: 0.799 AC: 32835 AN: 41082

American (AMR) AF: 0.827 AC: 12560 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2754 AN: 3464

East Asian (EAS) AF: 0.644 AC: 3279 AN: 5092

South Asian (SAS) AF: 0.727 AC: 3427 AN: 4714

European-Finnish (FIN) AF: 0.852 AC: 8790 AN: 10320

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.828 AC: 56152 AN: 67794

Other (OTH) AF: 0.784 AC: 1646 AN: 2100

Alfa AF: 0.818 Hom.: 78613

Bravo AF: 0.810

Asia WGS AF: 0.689 AC: 2374 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.22
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9536318; hg19: chr13-53494694;