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NM_001130987.2(DYSF):c.3341G>A (p.Arg1114His)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000128947.6
Variation ID:
128947
Description:
single nucleotide variant
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NM_001130987.2(DYSF):c.3341G>A (p.Arg1114His)

Allele ID
134394
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p13.2
Genomic location
2: 71574310 (GRCh38) GRCh38 UCSC
2: 71801440 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.71801440G>A
NC_000002.12:g.71574310G>A
NM_001130987.2:c.3341G>A MANE Select NP_001124459.1:p.Arg1114His missense
... more HGVS
Protein change
R1096H, R1114H, R1082H, R1097H, R1128H, R1113H, R1083H, R1127H
Other names
-
Canonical SPDI
NC_000002.12:71574309:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00699 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00656
Exome Aggregation Consortium (ExAC) 0.00189
The Genome Aggregation Database (gnomAD) 0.00599
1000 Genomes Project 0.00699
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00684
The Genome Aggregation Database (gnomAD), exomes 0.00148
Links
ClinGen: CA152663
UniProtKB: O75923#VAR_061170
dbSNP: rs59915619
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Sep 22, 2016 RCV000116927.5
Benign 1 criteria provided, single submitter Nov 19, 2018 RCV000532523.5
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 4, 2020 RCV001086595.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
DYSF - - GRCh38
GRCh37
2066 2081

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000309670.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Nov 19, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143818.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Qualitative or quantitative defects of dysferlin
Allele origin: germline
Invitae
Accession: SCV000649657.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Sep 22, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000525220.4
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)
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: SCV001301078.1
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)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000151023.2
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)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs59915619...

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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 Jun 23, 2021