Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000129.4(F13A1):c.1766T>A (p.Leu589Gln)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jul 4, 2021)
Last evaluated:
Dec 1, 2020
Accession:
VCV000786407.9
Variation ID:
786407
Description:
single nucleotide variant
Help

NM_000129.4(F13A1):c.1766T>A (p.Leu589Gln)

Allele ID
710574
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6p25.1
Genomic location
6: 6167600 (GRCh38) GRCh38 UCSC
6: 6167833 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_549:g.158092T>A
LRG_549t1:c.1766T>A
NC_000006.11:g.6167833A>T
... more HGVS
Protein change
L589Q
Other names
-
Canonical SPDI
NC_000006.12:6167599:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00120 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00630
Exome Aggregation Consortium (ExAC) 0.00396
1000 Genomes Project 0.00120
The Genome Aggregation Database (gnomAD) 0.00430
Trans-Omics for Precision Medicine (TOPMed) 0.00358
The Genome Aggregation Database (gnomAD), exomes 0.00379
Links
dbSNP: rs5983
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 1, 2020 RCV000968459.5
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001162333.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
F13A1 - - GRCh38
GRCh37
162 200

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001115915.2
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Factor XIII, A subunit, deficiency of
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001324284.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
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
(Dec 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001249732.6
Submitted: (Jul 04, 2021)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
Identification of potential mutations and genomic alterations in the epithelial and spindle cell components of biphasic synovial sarcomas using a human exome SNP chip. Qi Y BMC medical genomics 2015 PMID: 26503545
Using information interaction to discover epistatic effects in complex diseases. Anunciação O PloS one 2013 PMID: 24194833

Text-mined citations for rs5983...

Help
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 Oct 07, 2021