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NM_001130987.2(DYSF):c.4377G>A (p.Gln1459=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000128948.8
Variation ID:
128948
Description:
single nucleotide variant
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NM_001130987.2(DYSF):c.4377G>A (p.Gln1459=)

Allele ID
134395
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p13.2
Genomic location
2: 71612796 (GRCh38) GRCh38 UCSC
2: 71839926 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.71839926G>A
NC_000002.12:g.71612796G>A
NG_008694.1:g.164174G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:71612795:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.01098 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00331
The Genome Aggregation Database (gnomAD) 0.01043
Trans-Omics for Precision Medicine (TOPMed) 0.01043
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01092
Trans-Omics for Precision Medicine (TOPMed) 0.01115
The Genome Aggregation Database (gnomAD), exomes 0.00246
The Genome Aggregation Database (gnomAD) 0.00981
1000 Genomes Project 0.01098
Links
ClinGen: CA152667
dbSNP: rs76576806
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Mar 3, 2016 RCV000116929.6
Benign 1 criteria provided, single submitter Feb 2, 2018 RCV000711561.4
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 8, 2020 RCV001080539.3
Benign 1 no assertion criteria provided Sep 16, 2020 RCV001271538.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
DYSF - - GRCh38
GRCh37
2111 2126

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000309686.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Mar 03, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000525308.4
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
(Feb 02, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000841940.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Qualitative or quantitative defects of dysferlin
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001303232.1
Submitted: (Feb 20, 2020)
Evidence details
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)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Qualitative or quantitative defects of dysferlin
Allele origin: germline
Invitae
Accession: SCV000649689.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000151030.2
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)
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Limb-girdle muscular dystrophy type 2B
Allele origin: germline
Natera, Inc.
Accession: SCV001452771.1
Submitted: (Dec 28, 2020)
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
Analysis of the DYSF mutational spectrum in a large cohort of patients. Krahn M Human mutation 2009 PMID: 18853459

Text-mined citations for rs76576806...

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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 Nov 27, 2021