rs10090117

Variant names:

• chr8-18523725-T-C
• rs10090117

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 0.197 in 152,154 control chromosomes in the GnomAD database, including 2,972 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 0.20 (2972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 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: 0.197 AC: 30006 AN: 152034 Hom.: 2970 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.197 AC: 30021 AN: 152154 Hom.: 2972 Cov.: 32 AF XY: 0.199 AC XY: 14810 AN XY: 74388

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.181

Alfa AF: 0.185 Hom.: 5363

Bravo AF: 0.192

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
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: rs10090117; hg19: chr8-18381235;