13-82469313-A-G

Position:

• chr13-82469313-A-G

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 0.329 in 151,140 control chromosomes in the GnomAD database, including 8,486 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 0.33 (8486 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.82469313A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49669 AN: 151020 Hom.: 8487 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.329 AC: 49681 AN: 151140 Hom.: 8486 Cov.: 31 AF XY: 0.327 AC XY: 24165 AN XY: 73854

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.379

Alfa AF: 0.332 Hom.: 1079

Bravo AF: 0.343

Asia WGS AF: 0.423 AC: 1470 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	1.4
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2876780; hg19: chr13-83043448;