12-25396088-C-T

Position:

• chr12-25396088-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 0.518 in 151,938 control chromosomes in the GnomAD database, including 20,694 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 0.52 (20694 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 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: 0.518 AC: 78594 AN: 151820 Hom.: 20649 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.518 AC: 78693 AN: 151938 Hom.: 20694 Cov.: 31 AF XY: 0.521 AC XY: 38652 AN XY: 74238

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.519

Alfa AF: 0.487 Hom.: 3669

Bravo AF: 0.523

Asia WGS AF: 0.507 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7296765; hg19: chr12-25549022;