NM_007078.3(LDB3):c.896+6669TC[11] AND not specified

Germline classification:: Likely benign (4 submissions)
Last evaluated:: Apr 29, 2016
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000036852.14

Allele description [Variation Report for NM_007078.3(LDB3):c.896+6669TC[11]]

NM_007078.3(LDB3):c.896+6669TC[11]

Gene:

LDB3:LIM domain binding 3 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_007078.3(LDB3):c.896+6669TC[11]

HGVS:

NC_000010.10:g.88458997_88459002del
NC_000010.11:g.86699241CT[11]
NG_008876.1:g.35678CT[11]
NM_001080114.2:c.755+6669TC[11]
NM_001080115.2:c.897-38TC[11]
NM_001080116.1:c.756-38TC[11]
NM_001171610.2:c.1100+6669TC[11]
NM_001171611.2:c.1101-38TC[11]
NM_001368063.1:c.897-38TC[11]
NM_001368064.1:c.896+6669TC[11]
NM_001368065.1:c.896+6669TC[11]
NM_001368066.1:c.755+6669TC[11]
NM_001368067.1:c.756-38TC[11]
NM_001368068.1:c.756-38TC[11]
NM_007078.3:c.896+6669TC[11]MANE SELECT
LRG_385t2:c.756-38TC[11]
LRG_385:g.35678CT[11]
NC_000010.10:g.88458997_88459002del
NC_000010.10:g.88458998CT[11]
NC_000010.10:g.88459020_88459025delCTCTCT
NM_001080116.1:c.756-15_756-10del
NM_001080116.1:c.756-15_756-10delCTCTCT
c.756-15_756-10delCTCTCT

Links:

dbSNP: rs71019410

NCBI 1000 Genomes Browser:

rs71019410

Molecular consequence:

NM_001080114.2:c.755+6669TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001080115.2:c.897-38TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001080116.1:c.756-38TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001171610.2:c.1100+6669TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001171611.2:c.1101-38TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001368063.1:c.897-38TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001368064.1:c.896+6669TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001368065.1:c.896+6669TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001368066.1:c.755+6669TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001368067.1:c.756-38TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_001368068.1:c.756-38TC[11] - intron variant - [Sequence Ontology: SO:0001627]
NM_007078.3:c.896+6669TC[11] - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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fatty acid oxidation complex subunit alpha FadB [Acinetobacter indicus]
fatty acid oxidation complex subunit alpha FadB [Acinetobacter indicus]
gi|1348969545|ref|WP_104471812.1|

Protein
molecular chaperone HtpG [Acinetobacter indicus]
molecular chaperone HtpG [Acinetobacter indicus]
gi|1348969553|ref|WP_104471820.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000060507	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Oct 20, 2011)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000595566	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 29, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001743060	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV001923879	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing

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	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	8	8	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000060507.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	8	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		8	not provided	8	not provided

From Genetic Services Laboratory, University of Chicago, SCV000595566.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001743060.3

#	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 Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001923879.1

#	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

Last Updated: Sep 29, 2024

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