rs7078439

Positions:

• chr10-126731415-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.93).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C10orf90	ENST00000657225.1	n.157+67137A>G		intron_variant

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

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.662

Alfa AF: 0.690 Hom.: 18932

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7078439; hg19: chr10-128419984;