chr10-126464816-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2
The NM_001350921.2(C10orf90):c.1705C>T(p.Arg569Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0021 in 1,614,044 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.011 ( 25 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 38 hom. )
Consequence
C10orf90
NM_001350921.2 stop_gained
NM_001350921.2 stop_gained
Scores
1
3
3
Clinical Significance
Conservation
PhyloP100: 3.77
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 -8 ACMG points.
PM4
?
Stoplost variant in NM_001350921.2 Downstream stopcodon found after 12 codons.
BP6
?
Variant 10-126464816-G-A is Benign according to our data. Variant chr10-126464816-G-A is described in ClinVar as [Benign]. Clinvar id is 709837.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0113 (1712/152158) while in subpopulation AFR AF= 0.0378 (1570/41490). AF 95% confidence interval is 0.0363. There are 25 homozygotes in gnomad4. There are 780 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C10orf90 | NM_001350921.2 | c.1705C>T | p.Arg569Ter | stop_gained | 5/10 | ENST00000488181.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C10orf90 | ENST00000488181.3 | c.1705C>T | p.Arg569Ter | stop_gained | 5/10 | 2 | NM_001350921.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0112 AC: 1703AN: 152040Hom.: 25 Cov.: 32
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GnomAD3 exomes AF: 0.00296 AC: 743AN: 251420Hom.: 17 AF XY: 0.00207 AC XY: 281AN XY: 135870
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GnomAD4 exome AF: 0.00115 AC: 1675AN: 1461886Hom.: 38 Cov.: 32 AF XY: 0.000990 AC XY: 720AN XY: 727244
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GnomAD4 genome ? AF: 0.0113 AC: 1712AN: 152158Hom.: 25 Cov.: 32 AF XY: 0.0105 AC XY: 780AN XY: 74384
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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 | Dec 31, 2019 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
Cadd
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Dann
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Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
MutationTaster
Benign
A;A;A;N
Vest4
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at