12-126787123-C-T

Position:

• chr12-126787123-C-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 0.807 in 152,206 control chromosomes in the GnomAD database, including 52,566 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 0.81 (52566 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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 (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122806 AN: 152088 Hom.: 52543 Cov.: 33

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.807 AC: 122865 AN: 152206 Hom.: 52566 Cov.: 33 AF XY: 0.815 AC XY: 60643 AN XY: 74428

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.844

Alfa AF: 0.895 Hom.: 32849

Bravo AF: 0.787

Asia WGS AF: 0.931 AC: 3236 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	1.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4765114; hg19: chr12-127271669;