NM_014709.4:c.10386T>C
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_014709.4(USP34):c.10386T>C(p.Ala3462Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,613,356 control chromosomes in the GnomAD database, including 177,584 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.47 ( 17238 hom., cov: 32)
Exomes 𝑓: 0.46 ( 160346 hom. )
Consequence
USP34
NM_014709.4 synonymous
NM_014709.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.341
Genes affected
USP34 (HGNC:20066): (ubiquitin specific peptidase 34) Enables cysteine-type endopeptidase activity and thiol-dependent deubiquitinase. Involved in positive regulation of canonical Wnt signaling pathway and protein K48-linked deubiquitination. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
AHSA2P (HGNC:20437): (activator of HSP90 ATPase homolog 2, pseudogene) Predicted to enable ATPase activator activity. Predicted to be involved in positive regulation of ATPase activity and protein folding. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 2-61188357-A-G is Benign according to our data. Variant chr2-61188357-A-G is described in ClinVar as [Benign]. Clinvar id is 1229915.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.341 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.472 AC: 71644AN: 151870Hom.: 17213 Cov.: 32
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GnomAD3 exomes AF: 0.441 AC: 110120AN: 249468Hom.: 25533 AF XY: 0.437 AC XY: 59173AN XY: 135350
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GnomAD4 exome AF: 0.463 AC: 676756AN: 1461368Hom.: 160346 Cov.: 69 AF XY: 0.458 AC XY: 333222AN XY: 727004
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GnomAD4 genome AF: 0.472 AC: 71716AN: 151988Hom.: 17238 Cov.: 32 AF XY: 0.474 AC XY: 35201AN XY: 74290
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
May 01, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at