chr3-179708794-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_003940.3(USP13):c.642C>T(p.Cys214=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00339 in 1,614,068 control chromosomes in the GnomAD database, including 177 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 88 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 89 hom. )
Consequence
USP13
NM_003940.3 synonymous
NM_003940.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.88
Genes affected
USP13 (HGNC:12611): (ubiquitin specific peptidase 13) Enables several functions, including BAT3 complex binding activity; chaperone binding activity; and cysteine-type peptidase activity. Involved in several processes, including maintenance of unfolded protein involved in ERAD pathway; regulation of cellular catabolic process; and regulation of transcription, DNA-templated. Acts upstream of or within protein deubiquitination and protein stabilization. Predicted to be located in nucleoplasm. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 3-179708794-C-T is Benign according to our data. Variant chr3-179708794-C-T is described in ClinVar as [Benign]. Clinvar id is 708775.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.88 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0612 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP13 | NM_003940.3 | c.642C>T | p.Cys214= | synonymous_variant | 6/21 | ENST00000263966.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP13 | ENST00000263966.8 | c.642C>T | p.Cys214= | synonymous_variant | 6/21 | 1 | NM_003940.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0179 AC: 2722AN: 152108Hom.: 86 Cov.: 32
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GnomAD3 exomes AF: 0.00484 AC: 1217AN: 251408Hom.: 42 AF XY: 0.00369 AC XY: 502AN XY: 135876
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GnomAD4 exome AF: 0.00187 AC: 2732AN: 1461842Hom.: 89 Cov.: 30 AF XY: 0.00160 AC XY: 1162AN XY: 727232
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GnomAD4 genome ? AF: 0.0180 AC: 2738AN: 152226Hom.: 88 Cov.: 32 AF XY: 0.0174 AC XY: 1297AN XY: 74428
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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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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at