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NM_001110556.2(FLNA):c.3876C>T (p.His1292=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Nov 30, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000195739.5
Variation ID:
195739
Description:
single nucleotide variant
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NM_001110556.2(FLNA):c.3876C>T (p.His1292=)

Allele ID
192900
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 154359835 (GRCh38) GRCh38 UCSC
X: 153588203 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.153588203G>A
NC_000023.11:g.154359835G>A
NM_001110556.2:c.3876C>T MANE Select NP_001104026.1:p.His1292= synonymous
... more HGVS
Protein change
-
Other names
p.H1292H:CAC>CAT
Canonical SPDI
NC_000023.11:154359834:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00099
The Genome Aggregation Database (gnomAD), exomes 0.00043
The Genome Aggregation Database (gnomAD) 0.00073
Exome Aggregation Consortium (ExAC) 0.00045
Trans-Omics for Precision Medicine (TOPMed) 0.00065
Links
ClinGen: CA302846
dbSNP: rs199917719
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 Sep 11, 2015 RCV000176381.4
Likely benign 1 criteria provided, single submitter Aug 13, 2015 RCV000617532.1
Likely benign 1 criteria provided, single submitter Jun 1, 2018 RCV000680540.1
Likely benign 1 criteria provided, single submitter Sep 9, 2019 RCV000718830.1
Benign 1 criteria provided, single submitter Jun 26, 2018 RCV000757311.3
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV001080814.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FLNA Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1479 1802

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Sep 11, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000594800.1
Submitted: (Jul 05, 2017)
Evidence details
Benign
(Jul 10, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000250339.11
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)
Likely benign
(Jun 01, 2018)
criteria provided, single submitter
Method: clinical testing
Connective tissue disorder
Allele origin: germline
Center for Human Genetics, Inc,Center for Human Genetics, Inc
Accession: SCV000807950.1
Submitted: (Jul 17, 2018)
Evidence details
Likely benign
(Aug 13, 2015)
criteria provided, single submitter
Method: clinical testing
cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000738382.2
Submitted: (Jul 30, 2018)
Evidence details
Publications
PubMed (1)
Comment:
Lines of evidence used in support of classification: Rarity in general population databases (dbsnp, esp, 1000 genomes),Other strong data supporting benign classification
Benign
(Apr 09, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000228029.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jun 26, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000885481.1
Submitted: (Oct 10, 2018)
Evidence details
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Oto-palato-digital syndrome, type II
Periventricular nodular heterotopia 1
Frontometaphyseal dysplasia
Melnick-Needles syndrome
Allele origin: germline
Invitae
Accession: SCV000556064.5
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(Sep 09, 2019)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000849694.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Other strong data supporting benign classification

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
Fetal phenotypes in otopalatodigital spectrum disorders. Naudion S Clinical genetics 2016 PMID: 26404489
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=FLNA - - - -

Text-mined citations for rs199917719...

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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 Aug 14, 2021