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NM_001110556.2(FLNA):c.1029C>T (p.Ser343=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(5);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
10 (Most recent: Aug 24, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000198468.14
Variation ID:
198468
Description:
single nucleotide variant
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NM_001110556.2(FLNA):c.1029C>T (p.Ser343=)

Allele ID
195629
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 154366598 (GRCh38) GRCh38 UCSC
X: 153594966 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.153594966G>A
NC_000023.11:g.154366598G>A
NM_001110556.2:c.1029C>T MANE Select NP_001104026.1:p.Ser343= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:154366597:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00026 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00079
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00060
1000 Genomes Project 0.00026
Trans-Omics for Precision Medicine (TOPMed) 0.00104
The Genome Aggregation Database (gnomAD) 0.00059
The Genome Aggregation Database (gnomAD), exomes 0.00092
Links
ClinGen: CA211152
dbSNP: rs199853721
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Oct 8, 2014 RCV000244567.1
Likely benign 1 criteria provided, single submitter Oct 8, 2014 RCV000720675.1
Likely benign 2 criteria provided, single submitter Dec 1, 2018 RCV000762689.5
Benign 1 criteria provided, single submitter Dec 7, 2020 RCV001082645.2
Conflicting interpretations of pathogenicity 5 criteria provided, conflicting interpretations Nov 26, 2018 RCV000192632.5
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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
1477 1800

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jul 18, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000247386.1
Submitted: (Sep 15, 2015)
Evidence details
Benign
(Mar 06, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000613321.1
Submitted: (Aug 17, 2017)
Evidence details
Benign
(Nov 05, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000250366.10
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
(Oct 08, 2014)
criteria provided, single submitter
Method: clinical testing
cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000319473.4
Submitted: (Jul 30, 2018)
Evidence details
Benign
(Apr 12, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000232140.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Nov 26, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001158013.1
Submitted: (Aug 05, 2019)
Evidence details
Likely benign
(Oct 08, 2014)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000851554.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Benign
(Dec 07, 2020)
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: SCV000287135.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Dec 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000893025.7
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001808180.1
Submitted: (Aug 24, 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=FLNA - - - -

Text-mined citations for rs199853721...

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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 25, 2021