chr10-126505010-T-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001350921.2(C10orf90):c.481A>C(p.Arg161=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 1,614,246 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0069 ( 11 hom., cov: 33)
Exomes 𝑓: 0.00091 ( 7 hom. )
Consequence
C10orf90
NM_001350921.2 synonymous
NM_001350921.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.523
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 10-126505010-T-G is Benign according to our data. Variant chr10-126505010-T-G is described in ClinVar as [Benign]. Clinvar id is 780918.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.523 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00688 (1048/152366) while in subpopulation AFR AF= 0.0235 (978/41590). AF 95% confidence interval is 0.0223. There are 11 homozygotes in gnomad4. There are 513 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C10orf90 | NM_001350921.2 | c.481A>C | p.Arg161= | synonymous_variant | 4/10 | ENST00000488181.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C10orf90 | ENST00000488181.3 | c.481A>C | p.Arg161= | synonymous_variant | 4/10 | 2 | NM_001350921.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00685 AC: 1043AN: 152248Hom.: 11 Cov.: 33
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GnomAD3 exomes AF: 0.00207 AC: 516AN: 249376Hom.: 5 AF XY: 0.00147 AC XY: 199AN XY: 134944
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GnomAD4 exome AF: 0.000908 AC: 1327AN: 1461880Hom.: 7 Cov.: 33 AF XY: 0.000800 AC XY: 582AN XY: 727244
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GnomAD4 genome ? AF: 0.00688 AC: 1048AN: 152366Hom.: 11 Cov.: 33 AF XY: 0.00688 AC XY: 513AN XY: 74514
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2018 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at