chr12-114843038-T-C

Variant names:

• chr12-114843038-T-C
• rs7954363

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;