rs1553915580

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

Scores

Not classified

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:2

Conservation

PhyloP100: 2.10
Variant links:
Genes affected

Genome browser will be placed here

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
TERCNR_001566.1 linkuse as main transcriptn.407_408delTCinsAA non_coding_transcript_exon_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
Telomerase-vertENST00000363312.1 linkuse as main transcriptn.394_395delTCinsAA non_coding_transcript_exon_variant 1/16
TERCENST00000602385.1 linkuse as main transcriptn.407_408delTCinsAA non_coding_transcript_exon_variant 1/16

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
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 submitterclinical testingDegerman lab, Umeå UniversityNov 23, 2017- -
Dyskeratosis congenita, autosomal dominant 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingMolecular Diagnostics Laboratory, M Health Fairview: University of MinnesotaFeb 17, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs1553915580; hg19: chr3-169482441; API