chr12-25323285-G-A

Position:

• chr12-25323285-G-A

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 0.795 in 152,146 control chromosomes in the GnomAD database, including 49,649 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 0.79 (49649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 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: 0.795 AC: 120845 AN: 152028 Hom.: 49629 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.795 AC: 120914 AN: 152146 Hom.: 49649 Cov.: 32 AF XY: 0.796 AC XY: 59179 AN XY: 74388

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.809

Alfa AF: 0.865 Hom.: 25138

Bravo AF: 0.780

Asia WGS AF: 0.792 AC: 2754 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
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: rs10505975; hg19: chr12-25476219;