rs10492082

Variant names:

• chr12-48032512-T-C
• rs10492082

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 0.185 in 152,226 control chromosomes in the GnomAD database, including 3,136 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 0.18 (3136 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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: 0.185 AC: 28095 AN: 152108 Hom.: 3138 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.185 AC: 28103 AN: 152226 Hom.: 3136 Cov.: 33 AF XY: 0.183 AC XY: 13599 AN XY: 74448

African (AFR) AF: 0.310 AC: 12884 AN: 41504

American (AMR) AF: 0.111 AC: 1693 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3472

East Asian (EAS) AF: 0.152 AC: 790 AN: 5182

South Asian (SAS) AF: 0.134 AC: 646 AN: 4828

European-Finnish (FIN) AF: 0.151 AC: 1607 AN: 10608

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9510 AN: 68012

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.150 Hom.: 3578

Bravo AF: 0.190

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.37
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10492082; hg19: chr12-48426295;