rs1553915580
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong
The NR_001566.1(TERC):n.407_408delTCinsAA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: not found (cov: 32)
Consequence
TERC
NR_001566.1 non_coding_transcript_exon
NR_001566.1 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.10
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-169764653-GA-TT is Pathogenic according to our data. Variant chr3-169764653-GA-TT is described in ClinVar as [Likely_pathogenic]. Clinvar id is 446379.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERC | NR_001566.1 | n.407_408delTCinsAA | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
Telomerase-vert | ENST00000363312.1 | n.394_395delTCinsAA | non_coding_transcript_exon_variant | 1/1 | 6 | |||||
TERC | ENST00000602385.1 | n.407_408delTCinsAA | non_coding_transcript_exon_variant | 1/1 | 6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 2 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Degerman lab, Umeå University | Nov 23, 2017 | - - |
Dyskeratosis congenita, autosomal dominant 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota | Feb 17, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at