rs199422281
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 3P and 1B. PM2PP5BP4
The ENST00000602385.3(TERC):n.323C>T 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. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TERC
ENST00000602385.3 non_coding_transcript_exon
ENST00000602385.3 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.10
Publications
4 publications found
Genes affected
TERC (HGNC:11727): (telomerase RNA component) Telomerase is a ribonucleoprotein polymerase that maintains telomere ends by addition of the telomere repeat TTAGGG. The enzyme consists of a protein component with reverse transcriptase activity, and an RNA component, encoded by this gene, that serves as a template for the telomere repeat. Telomerase expression plays a role in cellular senescence, as it is normally repressed in postnatal somatic cells resulting in progressive shortening of telomeres. Deregulation of telomerase expression in somatic cells may be involved in oncogenesis. Studies in mouse suggest that telomerase also participates in chromosomal repair, since de novo synthesis of telomere repeats may occur at double-stranded breaks. Mutations in this gene cause autosomal dominant dyskeratosis congenita, and may also be associated with some cases of aplastic anemia. [provided by RefSeq, Jul 2008]
TERC Gene-Disease associations (from GenCC):
- 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
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-169764738-G-A is Pathogenic according to our data. Variant chr3-169764738-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 39291.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.16). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERC | NR_001566.3 | n.323C>T | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 600218Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 327526
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
600218
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
327526
African (AFR)
AF:
AC:
0
AN:
17354
American (AMR)
AF:
AC:
0
AN:
41998
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20644
East Asian (EAS)
AF:
AC:
0
AN:
35376
South Asian (SAS)
AF:
AC:
0
AN:
68158
European-Finnish (FIN)
AF:
AC:
0
AN:
36566
Middle Eastern (MID)
AF:
AC:
0
AN:
3904
European-Non Finnish (NFE)
AF:
AC:
0
AN:
343844
Other (OTH)
AF:
AC:
0
AN:
32374
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Aplastic anemia Pathogenic:1
May 10, 2012
GeneReviews
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:curation
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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