NM_001099274.3(TINF2):c.81C>A (p.Cys27Ter) AND Dyskeratosis congenita

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 3, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002525744.3

Allele description [Variation Report for NM_001099274.3(TINF2):c.81C>A (p.Cys27Ter)]

NM_001099274.3(TINF2):c.81C>A (p.Cys27Ter)

Genes:

LOC130055403:ATAC-STARR-seq lymphoblastoid active region 8199 [Gene]
TINF2:TERF1 interacting nuclear factor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q12

Genomic location:

Preferred name:

NM_001099274.3(TINF2):c.81C>A (p.Cys27Ter)

HGVS:

NC_000014.9:g.24242252G>T
NG_016650.1:g.5423C>A
NM_001099274.3:c.81C>AMANE SELECT
NM_001363668.2:c.81C>A
NM_012461.3:c.81C>A
NP_001092744.1:p.Cys27Ter
NP_001350597.1:p.Cys27Ter
NP_036593.2:p.Cys27Ter
LRG_342t1:c.81C>A
LRG_342t2:c.81C>A
LRG_342:g.5423C>A
LRG_342p1:p.Cys27Ter
LRG_342p2:p.Cys27Ter
NC_000014.8:g.24711458G>T
NM_001099274.1:c.81C>A

Protein change:

C27*

Links:

dbSNP: rs1060499576

NCBI 1000 Genomes Browser:

rs1060499576

Molecular consequence:

NM_001099274.3:c.81C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001363668.2:c.81C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_012461.3:c.81C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003273919	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 3, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003273919

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 3, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003273919.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 417880). This variant has not been reported in the literature in individuals affected with TINF2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys27*) in the TINF2 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in TINF2 cause disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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