rs10510155

Positions:

• chr10-126635431-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• 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/exons	MANE	Protein	UniProt
C10orf90	NM_001350921.2	c.313+11134G>A		intron_variant		ENST00000488181.3	NP_001337850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C10orf90	ENST00000488181.3	c.313+11134G>A		intron_variant		2	NM_001350921.2	ENSP00000474558	P2
C10orf90	ENST00000657225.1	n.230+11134G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0419

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0303

Gnomad4 FIN AF: 0.0956

Gnomad4 NFE AF: 0.0692

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0656 Hom.: 169

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510155; hg19: chr10-128324000;