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NM_198253.3(TERT):c.777G>A (p.Pro259=) AND Dyskeratosis congenita

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Apr 18, 2023
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002256723.10

Allele description [Variation Report for NM_198253.3(TERT):c.777G>A (p.Pro259=)]

NM_198253.3(TERT):c.777G>A (p.Pro259=)

Gene:
TERT:telomerase reverse transcriptase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p15.33
Genomic location:
Preferred name:
NM_198253.3(TERT):c.777G>A (p.Pro259=)
HGVS:
  • NC_000005.10:g.1294109C>T
  • NG_009265.1:g.5939G>A
  • NM_001193376.3:c.777G>A
  • NM_198253.3:c.777G>AMANE SELECT
  • NP_001180305.1:p.Pro259=
  • NP_937983.2:p.Pro259=
  • LRG_343t1:c.777G>A
  • LRG_343:g.5939G>A
  • NC_000005.9:g.1294224C>T
  • NM_198253.2:c.777G>A
  • NR_149162.3:n.856G>A
  • NR_149163.3:n.856G>A
Links:
dbSNP: rs746036694
NCBI 1000 Genomes Browser:
rs746036694
Molecular consequence:
  • NR_149162.3:n.856G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_149163.3:n.856G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001193376.3:c.777G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_198253.3:c.777G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Dyskeratosis congenita
Identifiers:
MONDO: MONDO:0015780; MedGen: C0265965; OMIM: PS127550

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002533161Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)		Uncertain significance
(Aug 6, 2021) 		germlinecuration

Citation Link,

SCV005048983Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Apr 18, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Details of each submission

From Sema4, Sema4, SCV002533161.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Ambry Genetics, SCV005048983.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024