chr10-126483468-G-A

Variant names:

• chr10-126483468-G-A
• rs10901614
• NM_001350921.2:c.1535-18482C>T

Variant summary

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350921.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf90	NM_001350921.2	MANE Select	c.1535-18482C>T		intron	N/A	NP_001337850.1
	C10orf90	NM_001004298.4		c.1244-18482C>T		intron	N/A	NP_001004298.2
	C10orf90	NM_001350922.2		c.1534+20489C>T		intron	N/A	NP_001337851.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf90	ENST00000488181.3	TSL:2 MANE Select	c.1535-18482C>T		intron	N/A	ENSP00000474558.3
	C10orf90	ENST00000284694.11	TSL:1	c.1244-18482C>T		intron	N/A	ENSP00000284694.7
	C10orf90	ENST00000424927.5	TSL:1	c.160+20489C>T		intron	N/A	ENSP00000411609.1

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

African (AFR) AF: 0.399 AC: 16536 AN: 41476

American (AMR) AF: 0.149 AC: 2277 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3470

East Asian (EAS) AF: 0.174 AC: 898 AN: 5168

South Asian (SAS) AF: 0.131 AC: 630 AN: 4816

European-Finnish (FIN) AF: 0.146 AC: 1542 AN: 10596

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10166 AN: 67986

Other (OTH) AF: 0.188 AC: 398 AN: 2116

Alfa AF: 0.206 Hom.: 1212

Bravo AF: 0.227

Asia WGS AF: 0.145 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.84
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10901614; hg19: chr10-128172037;