12-25259195-T-C

Position:

• chr12-25259195-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 0.317 in 151,928 control chromosomes in the GnomAD database, including 7,814 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 0.32 (7814 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.25259195T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48154 AN: 151810 Hom.: 7796 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.317 AC: 48203 AN: 151928 Hom.: 7814 Cov.: 31 AF XY: 0.317 AC XY: 23574 AN XY: 74266

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.323

Alfa AF: 0.325 Hom.: 1001

Bravo AF: 0.323

Asia WGS AF: 0.347 AC: 1204 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	14
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11612828; hg19: chr12-25412129; COSMIC: COSV64597909;