rs1502812

Variant names:

• chr12-58172577-C-T
• rs1502812

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.304 AC: 12567 AN: 41390

American (AMR) AF: 0.199 AC: 3040 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1651 AN: 5158

South Asian (SAS) AF: 0.248 AC: 1189 AN: 4802

European-Finnish (FIN) AF: 0.267 AC: 2814 AN: 10528

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17286 AN: 67968

Other (OTH) AF: 0.226 AC: 476 AN: 2106

Alfa AF: 0.270 Hom.: 772

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1502812; hg19: chr12-58566360;