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NM_004006.3(DMD):c.10262+1G>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 25, 2021)
Last evaluated:
May 5, 2021
Accession:
VCV000094433.13
Variation ID:
94433
Description:
single nucleotide variant
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NM_004006.3(DMD):c.10262+1G>A

Allele ID
100333
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xp21.2
Genomic location
X: 31177931 (GRCh38) GRCh38 UCSC
X: 31196048 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_199:g.2166679G>A
LRG_199t1:c.10262+1G>A
NC_000023.11:g.31177931C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:31177930:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00026 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00108
Exome Aggregation Consortium (ExAC) 0.00027
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00057
1000 Genomes Project 0.00026
The Genome Aggregation Database (gnomAD) 0.00051
The Genome Aggregation Database (gnomAD), exomes 0.00024
Links
ClinGen: CA222274
dbSNP: rs145603325
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Nov 16, 2018 RCV000778896.2
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000990563.3
Likely benign 1 criteria provided, single submitter Jan 9, 2019 RCV000621654.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations May 5, 2021 RCV000723512.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
DMD Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
4833 5050

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 15, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000112320.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Nov 16, 2018)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 3B
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000915301.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The DMD c.10262+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. The variant … (more)
Likely benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Duchenne muscular dystrophy
Allele origin: unknown
Mendelics
Accession: SCV001141576.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Jun 27, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143740.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (5)
Likely benign
(Jan 09, 2019)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000737260.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (2)
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Uncertain significance
(Jan 01, 2016)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 3B
Allele origin: unknown
Centre for Mendelian Genomics,University Medical Centre Ljubljana
Accession: SCV001366470.2
Submitted: (Nov 24, 2020)
Evidence details
Comment:
This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PP3. This variant was detected in hemizygous state.
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Duchenne muscular dystrophy
Allele origin: germline
Invitae
Accession: SCV000625826.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(May 05, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000564939.3
Submitted: (Sep 25, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 30415094, 23871722, 23352160, 26743743, 26990548, 32013268, 30275481)

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
Sudden unexpected death in the young - Value of massive parallel sequencing in postmortem genetic analyses. Scheiper S Forensic science international 2018 PMID: 30415094
NGS-Based Assay for the Identification of Individuals Carrying Recessive Genetic Mutations in Reproductive Medicine. Abulí A Human mutation 2016 PMID: 26990548
Pitfalls of Multiple Ligation-Dependent Probe Amplifications in Detecting DMD Exon Deletions or Duplications. Kim MJ The Journal of molecular diagnostics : JMD 2016 PMID: 26743743
XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. Piton A American journal of human genetics 2013 PMID: 23871722
Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Lim ET Neuron 2013 PMID: 23352160
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=DMD - - - -

Text-mined citations for rs145603325...

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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 Oct 30, 2021