rs10491032

Variant names:

• chr10-128986060-T-G
• rs10491032

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 0.166 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0476 AC: 1979 AN: 41546

American (AMR) AF: 0.188 AC: 2871 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 685 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1695 AN: 5172

South Asian (SAS) AF: 0.245 AC: 1179 AN: 4814

European-Finnish (FIN) AF: 0.195 AC: 2063 AN: 10600

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14200 AN: 68004

Other (OTH) AF: 0.176 AC: 373 AN: 2116

Alfa AF: 0.195 Hom.: 5040

Bravo AF: 0.161

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.0
DANN	Benign	0.79
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10491032; hg19: chr10-130784324;