13-82469313-A-G

Variant names:

• chr13-82469313-A-G
• rs2876780

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 0.329 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.269 AC: 11141 AN: 41342

American (AMR) AF: 0.391 AC: 5914 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1534 AN: 3452

East Asian (EAS) AF: 0.512 AC: 2627 AN: 5126

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4812

European-Finnish (FIN) AF: 0.252 AC: 2665 AN: 10584

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23088 AN: 67402

Other (OTH) AF: 0.379 AC: 796 AN: 2098

Alfa AF: 0.329 Hom.: 1104

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2876780; hg19: chr13-83043448;