10-126642144-T-C

Variant names:

• chr10-126642144-T-C
• rs2842169
• NM_001350921.2:c.313+4421A>G

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+4421A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0922 in 152,110 control chromosomes in the GnomAD database, including 713 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 0.092 (713 hom., cov: 32)
• Consequence: C10orf90 NM_001350921.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0976 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+4421A>G		intron	N/A	NP_001337850.1
	C10orf90	NM_001350922.2		c.313+4421A>G		intron	N/A	NP_001337851.1
	C10orf90	NM_001350923.2		c.313+4421A>G		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+4421A>G		intron	N/A	ENSP00000474558.3
	C10orf90	ENST00000657225.1		n.230+4421A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14010 AN: 151992 Hom.: 709 Cov.: 32

Gnomad AFR AF: 0.0716

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.0286

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.0922 AC: 14022 AN: 152110 Hom.: 713 Cov.: 32 AF XY: 0.0943 AC XY: 7017 AN XY: 74384

African (AFR) AF: 0.0718 AC: 2979 AN: 41476

American (AMR) AF: 0.0987 AC: 1509 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0950 AC: 330 AN: 3472

East Asian (EAS) AF: 0.0285 AC: 147 AN: 5162

South Asian (SAS) AF: 0.0979 AC: 472 AN: 4820

European-Finnish (FIN) AF: 0.139 AC: 1466 AN: 10584

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6768 AN: 67996

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.0946 Hom.: 1037

Bravo AF: 0.0883

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.48
PhyloP100		0.26
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: rs2842169; hg19: chr10-128330713;