rs12425376

Positions:

• chr12-27975692-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 0.43 in 151,960 control chromosomes in the GnomAD database, including 14,464 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 0.43 (14464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

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 (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.430 AC: 65313 AN: 151842 Hom.: 14430 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.430 AC: 65412 AN: 151960 Hom.: 14464 Cov.: 32 AF XY: 0.430 AC XY: 31953 AN XY: 74274

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.418

Alfa AF: 0.392 Hom.: 12793

Bravo AF: 0.440

Asia WGS AF: 0.467 AC: 1622 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	15
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12425376; hg19: chr12-28128625;