NM_206937.2(LIG4):c.26C>T (p.Thr9Ile) AND not provided

Germline classification:: Likely benign (3 submissions)
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:: RCV001705586.3

Allele description [Variation Report for NM_206937.2(LIG4):c.26C>T (p.Thr9Ile)]

NM_206937.2(LIG4):c.26C>T (p.Thr9Ile)

Gene:

LIG4:DNA ligase 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q33.3

Genomic location:

Preferred name:

NM_206937.2(LIG4):c.26C>T (p.Thr9Ile)

Other names:

p.T9I:ACT>ATT

HGVS:

NC_000013.11:g.108211243G>A
NG_007396.1:g.9292C>T
NM_001098268.2:c.26C>T
NM_001330595.2:c.-149-27C>T
NM_001352598.2:c.26C>T
NM_001352599.2:c.26C>T
NM_001352600.2:c.26C>T
NM_001352601.2:c.26C>T
NM_001352602.2:c.26C>T
NM_001352603.1:c.26C>T
NM_001352604.2:c.89-27C>T
NM_001379095.1:c.26C>T
NM_002312.3:c.26C>T
NM_206937.2:c.26C>TMANE SELECT
NP_001091738.1:p.Thr9Ile
NP_001339527.1:p.Thr9Ile
NP_001339528.1:p.Thr9Ile
NP_001339529.1:p.Thr9Ile
NP_001339530.1:p.Thr9Ile
NP_001339531.1:p.Thr9Ile
NP_001339532.1:p.Thr9Ile
NP_001366024.1:p.Thr9Ile
NP_002303.2:p.Thr9Ile
NP_996820.1:p.Thr9Ile
LRG_79t1:c.26C>T
LRG_79:g.9292C>T
LRG_79p1:p.Thr9Ile
NC_000013.10:g.108863591G>A
NM_206937.1:c.26C>T
P49917:p.Thr9Ile

Protein change:

T9I; THR9ILE

Links:

UniProtKB: P49917#VAR_033884; OMIM: 601837.0006; dbSNP: rs1805388

NCBI 1000 Genomes Browser:

rs1805388

Molecular consequence:

NM_001330595.2:c.-149-27C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001352604.2:c.89-27C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001098268.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352598.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352599.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352600.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352601.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352602.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352603.1:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001379095.1:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002312.3:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_206937.2:c.26C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001930880	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002074688	GenomeConnect, ClinGen	no classification provided	not provided	unknown	phenotyping only
SCV005218253	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001930880

Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Likely benign

germline

clinical testing

SCV002074688

GenomeConnect, ClinGen

no classification provided

not provided

unknown

phenotyping only

SCV005218253

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	phenotyping only

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 Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001930880.1

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

#	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 GenomeConnect, ClinGen, SCV002074688.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	phenotyping only	not provided

Description

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing.

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

From Breakthrough Genomics, Breakthrough Genomics, SCV005218253.1

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

#	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

Last Updated: Sep 29, 2024

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