rs1502812

chr12-58172577-C-T

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 0.263 in 151,902 control chromosomes in the GnomAD database, including 5,379 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 0.26 (5379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39897 AN: 151784 Hom.: 5379 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.263 AC: 39918 AN: 151902 Hom.: 5379 Cov.: 32 AF XY: 0.261 AC XY: 19354 AN XY: 74218

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.226

Alfa AF: 0.261 Hom.: 472

Bravo AF: 0.257

Asia WGS AF: 0.274 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.4
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1502812; hg19: chr12-58566360;