chr13-82353439-A-G

Variant names:

• chr13-82353439-A-G
• rs9531328

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 0.626 in 151,800 control chromosomes in the GnomAD database, including 30,581 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 0.63 (30581 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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: 0.626 AC: 94892 AN: 151682 Hom.: 30531 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.626 AC: 95008 AN: 151800 Hom.: 30581 Cov.: 31 AF XY: 0.631 AC XY: 46837 AN XY: 74204

African (AFR) AF: 0.741 AC: 30692 AN: 41410

American (AMR) AF: 0.579 AC: 8829 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2002 AN: 3460

East Asian (EAS) AF: 0.944 AC: 4875 AN: 5166

South Asian (SAS) AF: 0.723 AC: 3482 AN: 4818

European-Finnish (FIN) AF: 0.551 AC: 5801 AN: 10534

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37338 AN: 67848

Other (OTH) AF: 0.637 AC: 1344 AN: 2110

Alfa AF: 0.575 Hom.: 33649

Bravo AF: 0.630

Asia WGS AF: 0.831 AC: 2886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.53
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9531328; hg19: chr13-82927574;