13-76914602-G-A

Variant names:

• chr13-76914602-G-A
• rs12431203

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 0.179 in 152,020 control chromosomes in the GnomAD database, including 2,500 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 0.18 (2500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27160 AN: 151898 Hom.: 2500 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.179 AC: 27171 AN: 152020 Hom.: 2500 Cov.: 32 AF XY: 0.180 AC XY: 13375 AN XY: 74302

African (AFR) AF: 0.168 AC: 6974 AN: 41426

American (AMR) AF: 0.209 AC: 3189 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1243 AN: 5174

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4824

European-Finnish (FIN) AF: 0.179 AC: 1885 AN: 10560

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11710 AN: 67974

Other (OTH) AF: 0.174 AC: 367 AN: 2106

Alfa AF: 0.174 Hom.: 9915

Bravo AF: 0.181

Asia WGS AF: 0.244 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.75
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs12431203; hg19: chr13-77488736;