VCV003359242.2 - ClinVar

NM_004006.3(DMD):c.9564-30A>G

Germline

Classification

no assertion criteria provided. Learn more about how ClinVar calculates review status.

Pathogenic

This classification is based on the single submission received

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_004006.3(DMD):c.9564-30A>G

Variation ID: 3359242 Accession: VCV003359242.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xp21.2 X: 31206697 (GRCh38) [ NCBI UCSC ] X: 31224814 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 13, 2024	Apr 13, 2025	May 20, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_004006.3:c.9564-30A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_000109.4:c.9540-30A>G		intron variant
NM_004006.2:c.9564-30A>G
NM_004009.3:c.9552-30A>G		intron variant
NM_004010.3:c.9195-30A>G		intron variant
NM_004011.4:c.5541-30A>G		intron variant
NM_004012.4:c.5532-30A>G		intron variant
NM_004013.3:c.2184-30A>G		intron variant
NM_004014.3:c.1377-30A>G		intron variant
NM_004015.3:c.360-30A>G		intron variant
NM_004016.3:c.360-30A>G		intron variant
NM_004017.3:c.360-30A>G		intron variant
NM_004018.3:c.360-30A>G		intron variant
NM_004019.3:c.360-30A>G		intron variant
NM_004020.4:c.2184-30A>G		intron variant
NM_004021.3:c.2184-30A>G		intron variant
NM_004022.3:c.2184-30A>G		intron variant
NM_004023.3:c.2184-30A>G		intron variant
NC_000023.11:g.31206697T>C
NC_000023.10:g.31224814T>C
NG_012232.1:g.2137913A>G
LRG_199:g.2137913A>G
LRG_199t1:c.9564-30A>G

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000023.11:31206696:T:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
DMD		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	10064	10364

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Becker muscular dystrophy	Pathogenic (1)	no assertion criteria provided	May 20, 2024	RCV004759780.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (May 20, 2024) C Contributing to aggregate classification	no assertion criteria provided Method: clinical testing	Becker muscular dystrophy Affected status: yes Allele origin: maternal	Undiagnosed Diseases Network, NIH Study: Undiagnosed Diseases Network (NIH), UDN Accession: SCV005368749.2 First in ClinVar: Oct 13, 2024 Last updated: Apr 13, 2025	Number of individuals with the variant: 2 Clinical Features: Autism (present) , Delayed speech and language development (present) , Pes planus (present) , Distal muscle weakness (present) , Exercise intolerance (present) , Proximal muscle weakness (present) , Necrotizing myopathy (present) , Mild global developmental delay (present) , Lower limb pain (present) , Retractile testis (present) , Extremely elevated creatine kinase (present) , Elevated circulating aspartate aminotransferase concentration (present) , Elevated circulating alanine aminotransferase concentration (present) Zygosity: Hemizygote, Compound Heterozygote Family history: yes Age: 10-19 years Sex: male Tissue: Blood

Germline Functional Evidence

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 germline classification of this variant

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

Text-mined citations for this variant ...

Record last updated Apr 13, 2025

ClinVar Genomic variation as it relates to human health

NM_004006.3(DMD):c.9564-30A>G

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...