NM_198253.3(TERT):c.1234C>T (p.His412Tyr) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Jun 1, 2024
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:: RCV000425346.27

Allele description [Variation Report for NM_198253.3(TERT):c.1234C>T (p.His412Tyr)]

NM_198253.3(TERT):c.1234C>T (p.His412Tyr)

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.1234C>T (p.His412Tyr)

HGVS:

NC_000005.10:g.1293652G>A
NG_009265.1:g.6396C>T
NM_001193376.3:c.1234C>T
NM_198253.3:c.1234C>TMANE SELECT
NP_001180305.1:p.His412Tyr
NP_937983.2:p.His412Tyr
NP_937983.2:p.His412Tyr
LRG_343t1:c.1234C>T
LRG_343:g.6396C>T
LRG_343p1:p.His412Tyr
NC_000005.9:g.1293767G>A
NM_198253.2:c.1234C>T
NR_149162.3:n.1313C>T
NR_149163.3:n.1313C>T
O14746:p.His412Tyr

Protein change:

H412Y; HIS412TYR

Links:

UniProtKB: O14746#VAR_025149; OMIM: 187270.0002; dbSNP: rs34094720

NCBI 1000 Genomes Browser:

rs34094720

Molecular consequence:

NM_001193376.3:c.1234C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_198253.3:c.1234C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_149162.3:n.1313C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_149163.3:n.1313C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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BB153562 RIKEN full-length enriched, 16 days neonate thymus Mus musculus cDNA cl...
BB153562 RIKEN full-length enriched, 16 days neonate thymus Mus musculus cDNA clone A130014O09 3', mRNA sequence
gi|16268099|gnl|dbEST|9907927|dbj|B 62.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000511855	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Nov 15, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001801383	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Aug 26, 2020)	germline	clinical testing	Citation Link,
SCV002010312	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 3, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004153872	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Jun 1, 2024)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	12	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000511855.1

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

Description

Converted during submission to Likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.003709	not provided	not provided

From GeneDx, SCV001801383.1

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

Description

This variant is associated with the following publications: (PMID: 28495692, 31871297, 31268371, 29483670, 29416752, 30791107, 15814878, 29146883, 19147845, 19760749, 26576048, 27153395, 27111861, 23716176, 18753630, 23901009, 18042801, 23538340)

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

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002010312.3

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

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

From CeGaT Center for Human Genetics Tuebingen, SCV004153872.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	12	not provided	not provided	clinical testing	not provided

Description

TERT: BS1, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		12	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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