NM_016495.6(TBC1D7):c.200T>G (p.Leu67Trp) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Jan 17, 2024
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:: RCV000961688.9

Allele description [Variation Report for NM_016495.6(TBC1D7):c.200T>G (p.Leu67Trp)]

NM_016495.6(TBC1D7):c.200T>G (p.Leu67Trp)

Genes:

TBC1D7:TBC1 domain family member 7 [Gene - OMIM - HGNC]
TBC1D7-LOC100130357:TBC1D7-LOC100130357 readthrough [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

6p24.1

Genomic location:

Preferred name:

NM_016495.6(TBC1D7):c.200T>G (p.Leu67Trp)

HGVS:

NC_000006.12:g.13321089A>C
NG_033862.1:g.12495T>G
NM_001143964.4:c.200T>G
NM_001143965.4:c.200T>G
NM_001143966.4:c.119T>G
NM_001258457.3:c.200T>G
NM_001318805.2:c.200T>G
NM_001318806.2:c.119T>G
NM_001318809.2:c.200T>G
NM_016495.6:c.200T>GMANE SELECT
NP_001137436.1:p.Leu67Trp
NP_001137437.1:p.Leu67Trp
NP_001137437.1:p.Leu67Trp
NP_001137438.1:p.Leu40Trp
NP_001245386.1:p.Leu67Trp
NP_001305734.1:p.Leu67Trp
NP_001305735.1:p.Leu40Trp
NP_001305738.1:p.Leu67Trp
NP_057579.1:p.Leu67Trp
NC_000006.11:g.13321321A>C
NC_000006.11:g.13321321A>C
NM_001143965.3:c.200T>G
NM_016495.5:c.200T>G
NR_134872.2:n.290T>G

Protein change:

L40W

Links:

dbSNP: rs543580

NCBI 1000 Genomes Browser:

rs543580

Molecular consequence:

NM_001143964.4:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001143965.4:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001143966.4:c.119T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001258457.3:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318805.2:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318806.2:c.119T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318809.2:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_016495.6:c.200T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_134872.2:n.290T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001108740	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 17, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001798726	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001897260	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Dec 21, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001108740

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 17, 2024)

germline

clinical testing

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

SCV001798726

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus

no assertion criteria provided

Likely benign

germline

clinical testing

SCV001897260

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Dec 21, 2018)

germline

clinical testing

Citation Link

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	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, SCV001108740.4

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001798726.1

#	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 GeneDx, SCV001897260.1

#	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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