chr2-129106559-G-A

Variant names:

• chr2-129106559-G-A
• rs13428187

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 0.536 in 151,860 control chromosomes in the GnomAD database, including 24,644 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 0.54 (24644 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• 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 (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.536 AC: 81334 AN: 151742 Hom.: 24590 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.536 AC: 81443 AN: 151860 Hom.: 24644 Cov.: 31 AF XY: 0.535 AC XY: 39686 AN XY: 74200

African (AFR) AF: 0.835 AC: 34592 AN: 41424

American (AMR) AF: 0.461 AC: 7035 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1612 AN: 3460

East Asian (EAS) AF: 0.660 AC: 3401 AN: 5150

South Asian (SAS) AF: 0.407 AC: 1956 AN: 4808

European-Finnish (FIN) AF: 0.459 AC: 4824 AN: 10518

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26412 AN: 67934

Other (OTH) AF: 0.533 AC: 1125 AN: 2112

Alfa AF: 0.437 Hom.: 69104

Bravo AF: 0.554

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.68
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13428187; hg19: chr2-129864132;