rs10491032

chr10-128986060-T-G

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 0.166 in 152,216 control chromosomes in the GnomAD database, including 2,581 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 0.17 (2581 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 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: 0.166 AC: 25231 AN: 152098 Hom.: 2578 Cov.: 33

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.166 AC: 25244 AN: 152216 Hom.: 2581 Cov.: 33 AF XY: 0.169 AC XY: 12567 AN XY: 74418

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.176

Alfa AF: 0.200 Hom.: 4166

Bravo AF: 0.161

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	2.0
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491032; hg19: chr10-130784324;