chr10-126534012-G-A

Position:

• chr10-126534012-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.314-20073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,966 control chromosomes in the GnomAD database, including 27,228 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 0.58 (27228 hom., cov: 32)
• Consequence: C10orf90 NM_001350921.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C10orf90	NM_001350921.2	c.314-20073C>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.314-20073C>T		intron_variant		2	NM_001350921.2	ENSP00000474558	P2
C10orf90	ENST00000657225.1	n.231-20073C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87792 AN: 151848 Hom.: 27217 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.578 AC: 87824 AN: 151966 Hom.: 27228 Cov.: 32 AF XY: 0.581 AC XY: 43159 AN XY: 74266

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.611

Alfa AF: 0.604 Hom.: 4797

Bravo AF: 0.563

Asia WGS AF: 0.573 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.055
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1436804; hg19: chr10-128222581;