13-102876934-A-G

Variant names:

• chr13-102876934-A-G
• rs876430

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 0.603 in 151,720 control chromosomes in the GnomAD database, including 29,570 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 0.60 (29570 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91441 AN: 151600 Hom.: 29566 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.603 AC: 91474 AN: 151720 Hom.: 29570 Cov.: 31 AF XY: 0.603 AC XY: 44709 AN XY: 74122

African (AFR) AF: 0.355 AC: 14662 AN: 41298

American (AMR) AF: 0.650 AC: 9909 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2688 AN: 5158

South Asian (SAS) AF: 0.730 AC: 3504 AN: 4798

European-Finnish (FIN) AF: 0.645 AC: 6783 AN: 10510

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49234 AN: 67936

Other (OTH) AF: 0.620 AC: 1307 AN: 2108

Alfa AF: 0.691 Hom.: 63277

Bravo AF: 0.585

Asia WGS AF: 0.581 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs876430; hg19: chr13-103529284; COSMIC: COSV107450849;