rs1410763

chr13-86533124-A-Cchr13-86533124-A-T

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 0.644 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.627

Alfa AF: 0.592 Hom.: 11671

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1410763; hg19: chr13-87185379;