rs10492082

Variant names:

• chr12-48032512-T-C
• rs10492082

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 0.185 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.161

Alfa AF: 0.144 Hom.: 2380

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492082; hg19: chr12-48426295;