1-235380119-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001287802.2(TBCE):c.-241C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000933 in 1,607,288 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001287802.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBCE | ENST00000642610.2 | c.70C>T | p.Arg24Cys | missense_variant | Exon 2 of 17 | NM_003193.5 | ENSP00000494796.1 | |||
ENSG00000285053 | ENST00000645655.1 | c.70C>T | p.Arg24Cys | missense_variant | Exon 5 of 20 | ENSP00000495202.1 |
Frequencies
GnomAD3 genomes AF: 0.0000200 AC: 3AN: 149828Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251438Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135892
GnomAD4 exome AF: 0.00000823 AC: 12AN: 1457460Hom.: 0 Cov.: 32 AF XY: 0.00000827 AC XY: 6AN XY: 725114
GnomAD4 genome AF: 0.0000200 AC: 3AN: 149828Hom.: 0 Cov.: 31 AF XY: 0.0000274 AC XY: 2AN XY: 72890
ClinVar
Submissions by phenotype
Hypoparathyroidism-retardation-dysmorphism syndrome Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at