chr2-129106559-G-A

Variant names:

• chr2-129106559-G-A
• rs13428187

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.536 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

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.533

Alfa AF: 0.416 Hom.: 27939

Bravo AF: 0.554

Asia WGS AF: 0.564 AC: 1960 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	0.11
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13428187; hg19: chr2-129864132;