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NM_001110556.2(FLNA):c.3035C>T (p.Ser1012Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Oct 10, 2018)
Last evaluated:
Aug 3, 2017
Accession:
VCV000093753.1
Variation ID:
93753
Description:
single nucleotide variant
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NM_001110556.2(FLNA):c.3035C>T (p.Ser1012Leu)

Allele ID
99656
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 154361480 (GRCh38) GRCh38 UCSC
X: 153589848 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P21333:p.Ser1012Leu
NC_000023.10:g.153589848G>A
NC_000023.11:g.154361480G>A
... more HGVS
Protein change
S1012L
Other names
p.S1012L:TCG>TTG
Functional consequence
-
Global minor allele frequency (GMAF)
0.04371 (A)

Allele frequency
1000 Genomes Project 0.04371
The Genome Aggregation Database (gnomAD) 0.03559
Trans-Omics for Precision Medicine (TOPMed) 0.04196
Exome Aggregation Consortium (ExAC) 0.01321
The Genome Aggregation Database (gnomAD), exomes 0.01107
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.04886
Links
UniProtKB: P21333#VAR_031310
dbSNP: rs17091204
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Jun 5, 2014 RCV000079690.11
Benign 2 criteria provided, multiple submitters, no conflicts May 21, 2017 RCV000224049.2
Benign 1 criteria provided, single submitter Aug 3, 2017 RCV000471541.2
Benign 1 criteria provided, single submitter Jul 20, 2015 RCV000621157.1
Likely benign 1 criteria provided, single submitter Nov 1, 2016 RCV000659660.1
Benign 1 criteria provided, single submitter Jul 20, 2015 RCV000715892.1
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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
939 1223

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Feb 11, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281340.1
Submitted: (May 19, 2016)
Evidence details
Benign
(Aug 03, 2017)
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: SCV000556066.2
Submitted: (Oct 05, 2017)
Evidence details
Benign
(Mar 21, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000168569.12
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
(Jun 05, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000111573.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/em...
Benign
(Jul 20, 2015)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000846724.2
Submitted: (Jul 30, 2018)
Evidence details
Comment:
Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence ... (more)
Benign
(May 21, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000603747.2
Submitted: (Oct 10, 2018)
Evidence details
Likely benign
(Jul 10, 2013)
criteria provided, single submitter
Method: clinical testing
Not specified
(X-linked inheritance)
Allele origin: germline
Claritas Genomics
Accession: SCV000222833.1
Submitted: (Apr 13, 2015)
Evidence details
Likely benign
(Nov 01, 2016)
criteria provided, single submitter
Method: clinical testing
Connective tissue disorder
Allele origin: germline
Center for Human Genetics, Inc
Accession: SCV000781503.1
Submitted: (Dec 20, 2017)
Evidence details
Benign
(Jul 20, 2015)
criteria provided, single submitter
Method: clinical testing
cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000738344.2
Submitted: (Jul 30, 2018)
Evidence details
Comment:
Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence ... (more)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(X-linked inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000151188.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated ... (more)

Citations for this variant

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

Record last updated Sep 10, 2019