10-126735304-G-T

Variant names:

• chr10-126735304-G-T
• rs10794108
• ENST00000657225.1:n.157+63248C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657225.1(C10orf90):​n.157+63248C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,162 control chromosomes in the GnomAD database, including 3,545 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 (3545 hom., cov: 33)
• Consequence: C10orf90 ENST00000657225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

C10orf90 (HGNC:26563): (chromosome 10 open reading frame 90) Predicted to enable histone deacetylase binding activity; microtubule binding activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle process; and response to ionizing radiation. Located in several cellular components, including cytoskeleton; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 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
C10orf90	ENST00000657225.1	n.157+63248C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29847 AN: 152044 Hom.: 3550 Cov.: 33

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.196 AC: 29838 AN: 152162 Hom.: 3545 Cov.: 33 AF XY: 0.193 AC XY: 14333 AN XY: 74376

Gnomad4 AFR AF: 0.0761

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.237

Alfa AF: 0.252 Hom.: 7021

Bravo AF: 0.195

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.24
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10794108; hg19: chr10-128423873;