2-129426209-C-T

Variant names:

• chr2-129426209-C-T
• rs6732952

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 0.455 in 152,028 control chromosomes in the GnomAD database, including 17,610 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 0.45 (17610 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 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: 0.455 AC: 69067 AN: 151910 Hom.: 17578 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.455 AC: 69153 AN: 152028 Hom.: 17610 Cov.: 33 AF XY: 0.455 AC XY: 33815 AN XY: 74324

African (AFR) AF: 0.679 AC: 28133 AN: 41456

American (AMR) AF: 0.470 AC: 7179 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1309 AN: 3468

East Asian (EAS) AF: 0.670 AC: 3464 AN: 5168

South Asian (SAS) AF: 0.373 AC: 1798 AN: 4822

European-Finnish (FIN) AF: 0.364 AC: 3849 AN: 10562

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.324 AC: 22038 AN: 67970

Other (OTH) AF: 0.457 AC: 966 AN: 2112

Alfa AF: 0.351 Hom.: 5276

Bravo AF: 0.474

Asia WGS AF: 0.555 AC: 1929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.91
DANN	Benign	0.49
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs6732952; hg19: chr2-130183782;