rs12492285

Variant names:

• chr3-143234753-C-A
• rs12492285

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 0.138 in 152,204 control chromosomes in the GnomAD database, including 1,750 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 0.14 (1750 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.138 AC: 20981 AN: 152086 Hom.: 1751 Cov.: 33

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.138 AC: 20987 AN: 152204 Hom.: 1750 Cov.: 33 AF XY: 0.139 AC XY: 10359 AN XY: 74428

Gnomad4 AFR AF: 0.0817

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.159

Alfa AF: 0.133 Hom.: 404

Bravo AF: 0.147

Asia WGS AF: 0.243 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12492285; hg19: chr3-142953595;