rs11245052

Positions:

• chr10-126579071-T-A

Variant summary

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

The NM_001350921.2(C10orf90):​c.314-65132A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 142,420 control chromosomes in the GnomAD database, including 7,739 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 0.33 (7739 hom., cov: 28)
• Consequence: C10orf90 NM_001350921.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf90	NM_001350921.2	c.314-65132A>T		intron_variant		ENST00000488181.3	NP_001337850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C10orf90	ENST00000488181.3	c.314-65132A>T		intron_variant		2	NM_001350921.2	ENSP00000474558	P2
C10orf90	ENST00000657225.1	n.231-65132A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.326 AC: 46386 AN: 142314 Hom.: 7733 Cov.: 28

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.326 AC: 46413 AN: 142420 Hom.: 7739 Cov.: 28 AF XY: 0.323 AC XY: 22444 AN XY: 69452

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.318

Alfa AF: 0.342 Hom.: 1115

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11245052; hg19: chr10-128267640;