12-114646254-A-G

Position:

• chr12-114646254-A-G

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 0.718 in 151,678 control chromosomes in the GnomAD database, including 40,070 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 (40070 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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 = 0.882 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: 0.718 AC: 108839 AN: 151560 Hom.: 40021 Cov.: 30

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.718 AC: 108943 AN: 151678 Hom.: 40070 Cov.: 30 AF XY: 0.712 AC XY: 52790 AN XY: 74098

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.670

Alfa AF: 0.678 Hom.: 4188

Bravo AF: 0.727

Asia WGS AF: 0.659 AC: 2293 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	0.80
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61933115; hg19: chr12-115084059;