12-131327953-G-A

Variant names:

• chr12-131327953-G-A
• rs4759915

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 0.457 in 151,790 control chromosomes in the GnomAD database, including 16,505 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 0.46 (16505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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: 0.457 AC: 69260 AN: 151672 Hom.: 16483 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.457 AC: 69313 AN: 151790 Hom.: 16505 Cov.: 32 AF XY: 0.462 AC XY: 34288 AN XY: 74160

African (AFR) AF: 0.394 AC: 16311 AN: 41356

American (AMR) AF: 0.563 AC: 8592 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3466

East Asian (EAS) AF: 0.614 AC: 3157 AN: 5138

South Asian (SAS) AF: 0.515 AC: 2473 AN: 4806

European-Finnish (FIN) AF: 0.487 AC: 5133 AN: 10550

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30889 AN: 67906

Other (OTH) AF: 0.466 AC: 983 AN: 2108

Alfa AF: 0.456 Hom.: 10968

Bravo AF: 0.460

Asia WGS AF: 0.569 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.49
DANN	Benign	0.47
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4759915; hg19: chr12-131812498;