chr13-45337574-A-G
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003295.4(TPT1):c.517-186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000022 in 1,455,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000022 ( 0 hom. )
Consequence
TPT1
NM_003295.4 intron
NM_003295.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.95
Genes affected
TPT1 (HGNC:12022): (tumor protein, translationally-controlled 1) This gene encodes a protein that is a regulator of cellular growth and proliferation. Its mRNA is highly structured and contains an oligopyrimidine tract (5'-TOP) in its 5' untranslated region that functions to repress its translation under quiescent conditions. The encoded protein is involved in a variety of cellular pathways, including apoptosis, protein synthesis and cell division. It binds to and stabilizes microtubules, and removal of this protein through phosphorylation is required for progression through mitotic and meiotic cell divisions. This gene is known to play a role in carcinogenesis, and is upregulated in some cancer cells. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BS2
High AC in GnomAdExome4 at 32 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TPT1 | NM_003295.4 | c.517-186T>C | intron_variant | Intron 5 of 5 | ENST00000530705.6 | NP_003286.1 | ||
| TPT1 | NM_001286272.2 | c.517-21T>C | intron_variant | Intron 5 of 5 | NP_001273201.1 | |||
| TPT1 | NM_001286273.2 | c.415-186T>C | intron_variant | Intron 4 of 4 | NP_001273202.1 | |||
| SNORA31 | NR_002967.1 | n.36T>C | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000826 AC: 2AN: 242154Hom.: 0 AF XY: 0.00000755 AC XY: 1AN XY: 132514
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GnomAD4 exome AF: 0.0000220 AC: 32AN: 1455794Hom.: 0 Cov.: 30 AF XY: 0.0000152 AC XY: 11AN XY: 724496
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GnomAD4 genome
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32
Bravo
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ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Encephalopathy, acute, infection-induced (herpes-specific), susceptibility to, 10 Other:1
Jul 01, 2021
OMIM
Significance: risk factor
Review Status: no assertion criteria provided
Collection Method: literature only
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Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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