rs4962347

chr10-126609535-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+37030G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,132 control chromosomes in the GnomAD database, including 13,230 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 0.39 (13230 hom., cov: 33)
• Consequence: C10orf90 NM_001350921.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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]

LOC105378548 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C10orf90	NM_001350921.2	c.313+37030G>A		intron_variant		ENST00000488181.3
LOC105378548	XR_001747638.2	n.940-3C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C10orf90	ENST00000488181.3	c.313+37030G>A		intron_variant		2	NM_001350921.2	P2
C10orf90	ENST00000657225.1	n.230+37030G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59807 AN: 152016 Hom.: 13201 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.394 AC: 59879 AN: 152132 Hom.: 13230 Cov.: 33 AF XY: 0.398 AC XY: 29567 AN XY: 74360

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.373

Alfa AF: 0.306 Hom.: 15306

Bravo AF: 0.400

Asia WGS AF: 0.418 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.35
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4962347; hg19: chr10-128298104;