chr13-81261892-G-A

Position:

• chr13-81261892-G-A

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 0.844 in 150,194 control chromosomes in the GnomAD database, including 53,630 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 0.84 (53630 hom., cov: 27)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.81261892G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000229309	ENST00000458480.2	n.48+11407G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.844 AC: 126721 AN: 150090 Hom.: 53606 Cov.: 27

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.735

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.844 AC: 126792 AN: 150194 Hom.: 53630 Cov.: 27 AF XY: 0.843 AC XY: 61713 AN XY: 73244

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.811

Alfa AF: 0.870 Hom.: 60260

Bravo AF: 0.838

Asia WGS AF: 0.727 AC: 2523 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1287526; hg19: chr13-81836027;