rs12492285

Positions:

• chr3-143234753-C-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 0.138 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;