10-126672112-C-G

Variant names:

• chr10-126672112-C-G
• rs7909756
• ENST00000657225.1:n.158-25475G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657225.1(C10orf90):​n.158-25475G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,858 control chromosomes in the GnomAD database, including 7,848 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 0.32 (7848 hom., cov: 31)
• Consequence: C10orf90 ENST00000657225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 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.158-25475G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48596 AN: 151740 Hom.: 7839 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.320 AC: 48640 AN: 151858 Hom.: 7848 Cov.: 31 AF XY: 0.324 AC XY: 24042 AN XY: 74194

African (AFR) AF: 0.362 AC: 15010 AN: 41420

American (AMR) AF: 0.290 AC: 4433 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1057 AN: 5116

South Asian (SAS) AF: 0.398 AC: 1915 AN: 4810

European-Finnish (FIN) AF: 0.343 AC: 3610 AN: 10540

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20158 AN: 67928

Other (OTH) AF: 0.331 AC: 698 AN: 2106

Alfa AF: 0.163 Hom.: 295

Bravo AF: 0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7909756; hg19: chr10-128360681;