VCV000009120.2 - ClinVar

NC_000011.10:g.(68906754_68906786)_(68925257_68925289)del

Germline

Classification

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.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000011.10:g.(68906754_68906786)_(68925257_68925289)del

Variation ID: 9120 Accession: VCV000009120.2

Type and length

Deletion, 18,536 bp

Location

Cytogenetic: 11q13.3 11: 68906754-68925289 (GRCh38) [ NCBI UCSC ] 11: 68674222-68692757 (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, 2016	Oct 21, 2023	Oct 17, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NC_000011.10:g.(68906754_68906786)_(68925257_68925289)del
NC_000011.9:g.(68674222_68674254)_(68692725_68692757)del

Protein change

Other names

18.5-KB DEL, EX3-7

Canonical SPDI

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

dbVar: nssv7487143 dbVar: nsv1197514 OMIM: 600502.0009 VarSome

Comment on variant

Genomic deletion spanning homologous Alu sequences in introns 2 and 7 results in transcript with deletion of exons 3-7.

NCBI staff reviewed the sequence information reported in PubMed 15290238 Fig. 3D to determine the genomic location of this deletion on the current reference sequence.

18.5-kb genomic deletion beginning in intron 2 and ending in intron 7 of gene IGHMBP2 in regions of Alu repeats, causing deletion of exons 3-7 in the transcript.

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.
IGHMBP2		-	-	GRCh38 GRCh37	1337	1417

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.
Autosomal recessive distal spinal muscular atrophy 1	Pathogenic (1)	no assertion criteria provided	Oct 17, 2023	RCV000009690.6

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 (Oct 17, 2023)	no assertion criteria provided Method: literature only	NEURONOPATHY, DISTAL HEREDITARY MOTOR, AUTOSOMAL RECESSIVE 1 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000029908.5 First in ClinVar: Apr 04, 2013 Last updated: Oct 21, 2023	Publications: PubMed (1) PubMed: 17431882 Comment on evidence: For discussion of the 18.5-kb deletion in the IGHMBP2 gene that was found in compound heterozygous state in a patient with autosomal recessive distal hereditary … (more) For discussion of the 18.5-kb deletion in the IGHMBP2 gene that was found in compound heterozygous state in a patient with autosomal recessive distal hereditary motor neuronopathy-1 (HMNR1; 604320) by Guenther et al. (2004), see 600502.0008. (less)

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

Title	Author	Journal	Year	Link
Clinical and mutational profile in spinal muscular atrophy with respiratory distress (SMARD): defining novel phenotypes through hierarchical cluster analysis.	Guenther UP	Human mutation	2007	PMID: 17431882

Text-mined citations for this variant ...

Record last updated Oct 28, 2023

ClinVar Genomic variation as it relates to human health

NC_000011.10:g.(68906754_68906786)_(68925257_68925289)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...