chr3-169764870-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_001566.3(TERC):n.191C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000495 in 606,462 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 Uncertain significance (★).
Frequency
Consequence
NR_001566.3 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERC | NR_001566.3 | n.191C>T | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000463 AC: 1AN: 215772Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 119922
GnomAD4 exome AF: 0.00000495 AC: 3AN: 606462Hom.: 0 Cov.: 0 AF XY: 0.00000302 AC XY: 1AN XY: 331210
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
DNA sequence analysis of the TERC gene demonstrated a sequence change in exon 1, n.191C>T. This change does not appear to have been previously described in individuals with TERC-related disorders. This sequence change has been described in the gnomAD database in one individual which corresponds to a population frequency of 0.00046% (dbSNP rs756967332). This sequence change affects a poorly conserved nucleotide located in a domain that is not known to be functional. The functional significance of this sequence change is not known at present and its contribution to this individual's disease phenotype cannot definitively be determined. -
Dyskeratosis congenita, autosomal dominant 1 Uncertain:1
This variant occurs in the TERC gene, which encodes an RNA molecule that does not result in a protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with TERC-related conditions. ClinVar contains an entry for this variant (Variation ID: 465763). This variant is located within the template/pseudoknot domain of the TERC RNA component, which is required for RNA or RNP stability (PMID: 15082312, 21844345). This variant is located in a region of TERC in which a significant number of disease causing variants have been reported (PMID: 15082312, 21844345, 21931702). These observations suggest that this may be a clinically significant region. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at