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NM_001083962.2(TCF4):c.1923G>A (p.Glu641=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 18, 2020
Accession:
VCV000093543.8
Variation ID:
93543
Description:
single nucleotide variant
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NM_001083962.2(TCF4):c.1923G>A (p.Glu641=)

Allele ID
99448
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
18q21.2
Genomic location
18: 55228318 (GRCh38) GRCh38 UCSC
18: 52895549 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000018.10:g.55228318C>T
NC_000018.9:g.52895549C>T
NG_011716.2:g.412676G>A
... more HGVS
Protein change
-
Other names
p.E641E:GAG>GAA
Canonical SPDI
NC_000018.10:55228317:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00040
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD) 0.00022
The Genome Aggregation Database (gnomAD), exomes 0.00047
Trans-Omics for Precision Medicine (TOPMed) 0.00076
Links
ClinGen: CA295458
dbSNP: rs76956936
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Jan 7, 2016 RCV000150096.7
Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 18, 2020 RCV000280945.7
Likely benign 1 criteria provided, single submitter Sep 19, 2016 RCV000717018.1
Benign 1 criteria provided, single submitter Dec 31, 2018 RCV000858710.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TCF4 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
623 733

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Aug 10, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000195183.2
Submitted: (Sep 15, 2015)
Evidence details
Benign
(May 22, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171985.12
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Jan 07, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000111338.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 31, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001146124.1
Submitted: (Sep 25, 2019)
Evidence details
Likely benign
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Pitt-Hopkins syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000409524.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Sep 19, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000847863.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Likely benign
(Nov 18, 2020)
criteria provided, single submitter
Method: clinical testing
Pitt-Hopkins syndrome
Allele origin: germline
Invitae
Accession: SCV000646121.5
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TCF4 - - - -

Text-mined citations for rs76956936...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 26, 2021