rs10510155

Variant names:

• chr10-126635431-C-T
• rs10510155
• NM_001350921.2:c.313+11134G>A

Variant summary

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

The NM_001350921.2(C10orf90):​c.313+11134G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 152,134 control chromosomes in the GnomAD database, including 299 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 0.059 (299 hom., cov: 32)
• Consequence: C10orf90 NM_001350921.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C10orf90	NM_001350921.2	c.313+11134G>A		intron_variant	Intron 2 of 9	ENST00000488181.3	NP_001337850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C10orf90	ENST00000488181.3	c.313+11134G>A		intron_variant	Intron 2 of 9	2	NM_001350921.2	ENSP00000474558.3
C10orf90	ENST00000657225.1	n.230+11134G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8983 AN: 152016 Hom.: 300 Cov.: 32

Gnomad AFR AF: 0.0420

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0299

Gnomad FIN AF: 0.0956

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0692

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0590 AC: 8982 AN: 152134 Hom.: 299 Cov.: 32 AF XY: 0.0599 AC XY: 4457 AN XY: 74370

African (AFR) AF: 0.0419 AC: 1738 AN: 41504

American (AMR) AF: 0.0601 AC: 919 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.0303 AC: 146 AN: 4814

European-Finnish (FIN) AF: 0.0956 AC: 1010 AN: 10566

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0692 AC: 4709 AN: 68008

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0657 Hom.: 192

Bravo AF: 0.0551

Asia WGS AF: 0.0140 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.80
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10510155; hg19: chr10-128324000;