rs12618119

chr2-126742262-G-Achr2-126742262-G-T

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 0.719 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.698

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.3
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12618119; hg19: chr2-127499838;