17-16381964-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_018955.4(UBB):c.57C>T(p.Pro19Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00188 in 1,614,126 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0097 ( 26 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 16 hom. )
Consequence
UBB
NM_018955.4 synonymous
NM_018955.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.680
Genes affected
UBB (HGNC:12463): (ubiquitin B) This gene encodes ubiquitin, one of the most conserved proteins known. Ubiquitin has a major role in targeting cellular proteins for degradation by the 26S proteosome. It is also involved in the maintenance of chromatin structure, the regulation of gene expression, and the stress response. Ubiquitin is synthesized as a precursor protein consisting of either polyubiquitin chains or a single ubiquitin moiety fused to an unrelated protein. This gene consists of three direct repeats of the ubiquitin coding sequence with no spacer sequence. Consequently, the protein is expressed as a polyubiquitin precursor with a final amino acid after the last repeat. An aberrant form of this protein has been detected in patients with Alzheimer's disease and Down syndrome. Pseudogenes of this gene are located on chromosomes 1, 2, 13, and 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
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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=-0.5).
BP6
Variant 17-16381964-C-T is Benign according to our data. Variant chr17-16381964-C-T is described in ClinVar as [Benign]. Clinvar id is 716463.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.68 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00968 (1474/152272) while in subpopulation AFR AF= 0.0338 (1406/41538). AF 95% confidence interval is 0.0324. There are 26 homozygotes in gnomad4. There are 680 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1474 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00967 AC: 1472AN: 152154Hom.: 26 Cov.: 32
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GnomAD3 exomes AF: 0.00283 AC: 711AN: 251482Hom.: 8 AF XY: 0.00204 AC XY: 277AN XY: 135922
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GnomAD4 exome AF: 0.00107 AC: 1559AN: 1461854Hom.: 16 Cov.: 30 AF XY: 0.000925 AC XY: 673AN XY: 727228
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GnomAD4 genome AF: 0.00968 AC: 1474AN: 152272Hom.: 26 Cov.: 32 AF XY: 0.00913 AC XY: 680AN XY: 74458
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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
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
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