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NM_000169.3(GLA):c.639+6A>C

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: May 19, 2020)
Last evaluated:
Mar 30, 2019
Accession:
VCV000042457.4
Variation ID:
42457
Description:
single nucleotide variant
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NM_000169.3(GLA):c.639+6A>C

Allele ID
51627
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq22.1
Genomic location
X: 101400660 (GRCh38) GRCh38 UCSC
X: 100655648 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.100655648T>G
NC_000023.11:g.101400660T>G
NM_000169.3:c.639+6A>C MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:101400659:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00026 (G)

Allele frequency
1000 Genomes Project 0.00026
Exome Aggregation Consortium (ExAC) 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00003
Links
dbSNP: rs200096940
ClinGen: CA021876
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 3 criteria provided, multiple submitters, no conflicts Mar 30, 2019 RCV001165639.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 18, 2017 RCV000035306.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GLA Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
11 860
RPL36A-HNRNPH2 - - - GRCh38
GRCh37
- 865

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 18, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000728502.1
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)
Uncertain significance
(Dec 13, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000058954.5
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Variant classified as Uncertain Significance - Favor Benign. The 639+6A>C varian t (GLA) has not been previously reported but has been identified by our laborato … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Fabry disease
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001327853.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
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
(Mar 30, 2019)
criteria provided, single submitter
Method: clinical testing
Fabry disease
Allele origin: germline
Color Health, Inc
Accession: SCV001352031.1
Submitted: (May 19, 2020)
Evidence details
Uncertain significance
(Jan 22, 2020)
no assertion criteria provided
Method: curation
Fabry disease
(X-linked inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001422790.1
Submitted: (Mar 09, 2020)
Comment:
X-linked inheritance (primarily recessive with milder female expression)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.639+6A>C variant in GLA has been reported in at least 1 individual with Fabry disease (PMID:22805550), and has been identified in 0.005% (1/15710) and … (more)

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
Prevalence of Fabry disease in a predominantly hypertensive population with left ventricular hypertrophy. Terryn W International journal of cardiology 2013 PMID: 22805550
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/0dea803a-bf48-4877-8105-fc29a1c02971 - - - -

Text-mined citations for rs200096940...

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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 27, 2021