rs4962347

Variant names:

• chr10-126609535-C-T
• rs4962347
• NM_001350921.2:c.313+37030G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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]

LOC105378548 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.313+37030G>A		intron	N/A	NP_001337850.1
	C10orf90	NM_001350922.2		c.313+37030G>A		intron	N/A	NP_001337851.1
	C10orf90	NM_001350923.2		c.313+37030G>A		intron	N/A	NP_001337852.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf90	ENST00000488181.3	TSL:2 MANE Select	c.313+37030G>A		intron	N/A	ENSP00000474558.3
	C10orf90	ENST00000657225.1		n.230+37030G>A		intron	N/A

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

African (AFR) AF: 0.600 AC: 24878 AN: 41496

American (AMR) AF: 0.378 AC: 5780 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1205 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1358 AN: 5182

South Asian (SAS) AF: 0.447 AC: 2156 AN: 4828

European-Finnish (FIN) AF: 0.398 AC: 4208 AN: 10560

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19111 AN: 67998

Other (OTH) AF: 0.373 AC: 787 AN: 2112

Alfa AF: 0.324 Hom.: 28093

Bravo AF: 0.400

Asia WGS AF: 0.418 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.45
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4962347; hg19: chr10-128298104;