rs781517281
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000602385.3(TERC):n.7C>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 0.00000654 in 612,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000602385.3 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
Publications
- dyskeratosis congenita, autosomal dominant 1Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
- acute myeloid leukemiaInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERC | NR_001566.3 | n.7C>T | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000439 AC: 1AN: 227816 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000654 AC: 4AN: 612062Hom.: 0 Cov.: 0 AF XY: 0.00000897 AC XY: 3AN XY: 334446 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
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. This variant is located at the 5’ end of the TERC RNA component (PMID: 15082312, 21844345). The functional significance of this region is not well understood. 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