13-86533124-A-C

Variant names:

• chr13-86533124-A-C
• rs1410763

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 0.644 in 151,996 control chromosomes in the GnomAD database, including 32,017 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 0.64 (32017 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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: 0.644 AC: 97836 AN: 151878 Hom.: 31978 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.644 AC: 97933 AN: 151996 Hom.: 32017 Cov.: 31 AF XY: 0.641 AC XY: 47618 AN XY: 74288

African (AFR) AF: 0.767 AC: 31799 AN: 41482

American (AMR) AF: 0.635 AC: 9699 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1988 AN: 3462

East Asian (EAS) AF: 0.506 AC: 2602 AN: 5138

South Asian (SAS) AF: 0.559 AC: 2698 AN: 4824

European-Finnish (FIN) AF: 0.607 AC: 6419 AN: 10568

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40587 AN: 67948

Other (OTH) AF: 0.627 AC: 1321 AN: 2106

Alfa AF: 0.594 Hom.: 13286

Bravo AF: 0.653

Asia WGS AF: 0.605 AC: 2104 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.052
DANN	Benign	0.22
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1410763; hg19: chr13-87185379;