12-25840870-T-C

Position:

• chr12-25840870-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 0.189 in 151,818 control chromosomes in the GnomAD database, including 2,775 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 0.19 (2775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 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: 0.189 AC: 28732 AN: 151702 Hom.: 2777 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.189 AC: 28734 AN: 151818 Hom.: 2775 Cov.: 32 AF XY: 0.187 AC XY: 13898 AN XY: 74174

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.187

Alfa AF: 0.188 Hom.: 4282

Bravo AF: 0.187

Asia WGS AF: 0.183 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16929496; hg19: chr12-25993804;