rs582524

Variant names:

• chr13-33070400-G-A
• rs582524

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.558 in 151,892 control chromosomes in the GnomAD database, including 24,150 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 0.56 (24150 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.596 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: 0.558 AC: 84698 AN: 151774 Hom.: 24117 Cov.: 31

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.558 AC: 84789 AN: 151892 Hom.: 24150 Cov.: 31 AF XY: 0.561 AC XY: 41647 AN XY: 74214

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.572

Alfa AF: 0.563 Hom.: 5704

Bravo AF: 0.556

Asia WGS AF: 0.419 AC: 1462 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	1.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs582524; hg19: chr13-33644537;