rs7078439

Variant names:

• chr10-126731415-T-C
• rs7078439
• ENST00000657225.1:n.157+67137A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657225.1(C10orf90):​n.157+67137A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,098 control chromosomes in the GnomAD database, including 35,673 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 0.68 (35673 hom., cov: 33)
• Consequence: C10orf90 ENST00000657225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C10orf90	ENST00000657225.1	n.157+67137A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103619 AN: 151980 Hom.: 35648 Cov.: 33

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.682 AC: 103695 AN: 152098 Hom.: 35673 Cov.: 33 AF XY: 0.687 AC XY: 51038 AN XY: 74338

African (AFR) AF: 0.621 AC: 25746 AN: 41470

American (AMR) AF: 0.690 AC: 10546 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2135 AN: 3470

East Asian (EAS) AF: 0.853 AC: 4407 AN: 5168

South Asian (SAS) AF: 0.749 AC: 3604 AN: 4812

European-Finnish (FIN) AF: 0.746 AC: 7896 AN: 10582

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47179 AN: 67988

Other (OTH) AF: 0.662 AC: 1399 AN: 2112

Alfa AF: 0.692 Hom.: 27023

Bravo AF: 0.671

Asia WGS AF: 0.791 AC: 2749 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.76
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7078439; hg19: chr10-128419984;