10-126735304-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657225.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf90	ENST00000657225.1		n.157+63248C>A		intron	N/A

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

African (AFR) AF: 0.0761 AC: 3159 AN: 41534

American (AMR) AF: 0.224 AC: 3416 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3470

East Asian (EAS) AF: 0.110 AC: 570 AN: 5174

South Asian (SAS) AF: 0.188 AC: 906 AN: 4824

European-Finnish (FIN) AF: 0.199 AC: 2108 AN: 10574

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17764 AN: 67994

Other (OTH) AF: 0.237 AC: 502 AN: 2114

Alfa AF: 0.245 Hom.: 9175

Bravo AF: 0.195

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.24
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10794108; hg19: chr10-128423873;