12-25396088-C-T

Variant names:

• chr12-25396088-C-T
• rs7296765

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.610 AC: 25297 AN: 41444

American (AMR) AF: 0.528 AC: 8068 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1839 AN: 3472

East Asian (EAS) AF: 0.449 AC: 2321 AN: 5166

South Asian (SAS) AF: 0.555 AC: 2671 AN: 4814

European-Finnish (FIN) AF: 0.495 AC: 5206 AN: 10520

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31638 AN: 67936

Other (OTH) AF: 0.519 AC: 1095 AN: 2110

Alfa AF: 0.490 Hom.: 3801

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs7296765; hg19: chr12-25549022;