10-126483468-G-A

Position:

• chr10-126483468-G-A

Variant summary

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

The NM_001350921.2(C10orf90):​c.1535-18482C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,112 control chromosomes in the GnomAD database, including 4,530 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 0.22 (4530 hom., cov: 33)
• Consequence: C10orf90 NM_001350921.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C10orf90	NM_001350921.2	c.1535-18482C>T		intron_variant		ENST00000488181.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C10orf90	ENST00000488181.3	c.1535-18482C>T		intron_variant		2	NM_001350921.2	P2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33251 AN: 151994 Hom.: 4525 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.219 AC: 33283 AN: 152112 Hom.: 4530 Cov.: 33 AF XY: 0.216 AC XY: 16039 AN XY: 74368

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.188

Alfa AF: 0.225 Hom.: 682

Bravo AF: 0.227

Asia WGS AF: 0.145 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10901614; hg19: chr10-128172037;