VCV001458360.6 - ClinVar

NC_000016.9:g.(?_88717354)_(88718353_?)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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000016.9:g.(?_88717354)_(88718353_?)del

Variation ID: 1458360 Accession: VCV001458360.6

Type and length

Deletion, 1,000 bp

Location

Cytogenetic: 16q24.3 16: 88717354-88718353 (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	Mar 28, 2022	Nov 11, 2023	Oct 31, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000016.9:g.(?_88717354)_(88718353_?)del

Protein change

Other names

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

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.
CYBA		-	-	GRCh38 GRCh37	457	545
MVD		-	-	GRCh38 GRCh37	67	162

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.
Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative	Pathogenic (1)	criteria provided, single submitter	Oct 31, 2022	RCV001956331.5

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 31, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002243199.3 First in ClinVar: Mar 28, 2022 Last updated: Nov 11, 2023	Publications: PubMed (4) PubMed: 10910929‚ 20167518‚ 22876374‚ 23910690 Comment: This variant is a gross deletion of the genomic region encompassing exon(s) 1 of the CYBA gene, which includes the initiator codon. This deletion extends … (more) This variant is a gross deletion of the genomic region encompassing exon(s) 1 of the CYBA gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CYBA are known to be pathogenic (PMID: 10910929, 20167518, 22876374). A similar copy number variant has been observed in individual(s) with chronic granulomatous disease (PMID: 23910690). For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This variant is a gross deletion of the genomic region encompassing exon(s) 1 of the CYBA gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CYBA are known to be pathogenic (PMID: 10910929, 20167518, 22876374). A similar copy number variant has been observed in individual(s) with chronic granulomatous disease (PMID: 23910690). For these reasons, this variant has been classified as Pathogenic.

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Chronic Granulomatous Disease.	Adam MP	-	2022	PMID: 22876374
Clinical, functional, and genetic characterization of chronic granulomatous disease in 89 Turkish patients.	Köker MY	The Journal of allergy and clinical immunology	2013	PMID: 23910690
Hematologically important mutations: the autosomal recessive forms of chronic granulomatous disease (second update).	Roos D	Blood cells, molecules & diseases	2010	PMID: 20167518
Molecular analysis of 9 new families with chronic granulomatous disease caused by mutations in CYBA, the gene encoding p22(phox).	Rae J	Blood	2000	PMID: 10910929

Text-mined citations for this variant ...

Record last updated Dec 28, 2024

ClinVar Genomic variation as it relates to human health

NC_000016.9:g.(?_88717354)_(88718353_?)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...