12-25396088-C-T

Variant names:

• chr12-25396088-C-T
• rs7296765

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;