rs582091

Variant names:

• chr13-36928460-G-C
• rs582091

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 0.563 in 151,972 control chromosomes in the GnomAD database, including 24,614 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 (24614 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 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: 0.564 AC: 85571 AN: 151852 Hom.: 24606 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.563 AC: 85620 AN: 151972 Hom.: 24614 Cov.: 32 AF XY: 0.558 AC XY: 41430 AN XY: 74268

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.574

Alfa AF: 0.586 Hom.: 3256

Bravo AF: 0.557

Asia WGS AF: 0.371 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.083
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs582091; hg19: chr13-37502597;