2-126742262-G-A

Variant names:

• chr2-126742262-G-A
• rs12618119

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 0.719 in 152,156 control chromosomes in the GnomAD database, including 40,757 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 0.72 (40757 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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: 0.719 AC: 109258 AN: 152038 Hom.: 40708 Cov.: 33

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.719 AC: 109360 AN: 152156 Hom.: 40757 Cov.: 33 AF XY: 0.715 AC XY: 53187 AN XY: 74406

African (AFR) AF: 0.929 AC: 38602 AN: 41548

American (AMR) AF: 0.569 AC: 8692 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2542 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2815 AN: 5180

South Asian (SAS) AF: 0.644 AC: 3101 AN: 4812

European-Finnish (FIN) AF: 0.670 AC: 7100 AN: 10590

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44062 AN: 67976

Other (OTH) AF: 0.698 AC: 1468 AN: 2104

Alfa AF: 0.586 Hom.: 1819

Bravo AF: 0.721

Asia WGS AF: 0.631 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.84
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs12618119; hg19: chr2-127499838;