12-114843038-T-C

Position:

• chr12-114843038-T-C

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 0.122 in 152,188 control chromosomes in the GnomAD database, including 3,570 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 0.12 (3570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

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 = 0.405 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: 0.122 AC: 18571 AN: 152070 Hom.: 3555 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.00848

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00359

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.122 AC: 18630 AN: 152188 Hom.: 3570 Cov.: 32 AF XY: 0.117 AC XY: 8736 AN XY: 74410

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.0496

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.00848

Gnomad4 NFE AF: 0.00359

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.00847 Hom.: 33

Bravo AF: 0.141

Asia WGS AF: 0.0620 AC: 216 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	0.72
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7954363; hg19: chr12-115280843;