VCV000014053.1 - ClinVar

NC_000005.10:g.(159317671_159317673)_(159322312_159322314)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_000005.10:g.(159317671_159317673)_(159322312_159322314)del

Variation ID: 14053 Accession: VCV000014053.1

Type and length

Deletion, 4,640 bp

Location

Cytogenetic: 5q31.1-q33.1 5: 159317671-159322314 (GRCh38) [ 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	Jan 11, 2018	Jan 11, 2018	Dec 15, 1998

HGVS

Nucleotide	Protein	Molecular consequence
NC_000005.10:g.(159317671_159317673)_(159322312_159322314)del

Protein change

Other names

4.4-KB DEL

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: nssv7487232 dbVar: nsv1197523 OMIM: 161561.0001 VarSome

Comment on variant

NCBI staff reviewed the sequence information reported in PubMed 9854038 Fig. 3B to determine the location of this allele on the current reference sequence.

Deletion in IL12B spanning exons 5 and 6 plus flanking intronic sequences.

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.
IL12B		-	-	GRCh38 GRCh37	215	235

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.
Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency	Pathogenic (1)	no assertion criteria provided	Dec 15, 1998	RCV000015097.28

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 (Dec 15, 1998)	no assertion criteria provided Method: literature only	IMMUNODEFICIENCY 29 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000035354.4 First in ClinVar: Apr 04, 2013 Last updated: Jan 11, 2018	Publications: PubMed (1) PubMed: 9854038 Comment on evidence: In a Pakistani child of consanguineous parents, Altare et al. (1998) demonstrated that disseminated infection with BCG and Salmonella enteritidis (IMD29; 614890) was due to … (more) In a Pakistani child of consanguineous parents, Altare et al. (1998) demonstrated that disseminated infection with BCG and Salmonella enteritidis (IMD29; 614890) was due to homozygosity for a deletion within the IL12-p40 subunit gene. One sib had died at age 1 year with fever of unknown cause. The father suffered in childhood from severe and recurrent non-typhi salmonella (Salmonella bareilly) infection, requiring several prolonged courses of antibiotic therapy over 4 years. The gene encoding the p40 subunit was shown to consist of at least 7 exons, and a deletion of 4.4 kb encompassing 2 coding exons was found in the patient. Three nucleotides adjacent to the 2 recombination breakpoints were identical and may have contributed to the recombination process. The parents and a healthy sib were heterozygous for the deletion. (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
Inherited interleukin 12 deficiency in a child with bacille Calmette-Guérin and Salmonella enteritidis disseminated infection.	Altare F	The Journal of clinical investigation	1998	PMID: 9854038

Text-mined citations for this variant ...

Record last updated Apr 25, 2022

ClinVar Genomic variation as it relates to human health

NC_000005.10:g.(159317671_159317673)_(159322312_159322314)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...