GeneBe

chr3-169764630-G-C

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NR_001566.3(TERC):​n.431C>G 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 0.00000179 in 558,900 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

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000018 ( 0 hom. )

Consequence

TERC
NR_001566.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TERCNR_001566.3 linkn.431C>G non_coding_transcript_exon_variant Exon 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
Telomerase-vertENST00000363312.1 linkn.418C>G non_coding_transcript_exon_variant Exon 1 of 1 6
TERCENST00000602385.1 linkn.431C>G non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000179
AC:
1
AN:
558900
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
302194
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
15698
American (AMR)
AF:
0.00
AC:
0
AN:
35276
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
17862
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35202
South Asian (SAS)
AF:
0.00
AC:
0
AN:
64392
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
36506
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2620
European-Non Finnish (NFE)
AF:
0.00000311
AC:
1
AN:
321078
Other (OTH)
AF:
0.00
AC:
0
AN:
30266
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
9.0
DANN
Benign
0.66
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1374142931; hg19: chr3-169482418; API