VCV002422485.14 - ClinVar

NC_000009.11:g.(?_32453279)_(37785041_?)dup

Germline

Classification

criteria provided, single submitter. Learn more about how ClinVar calculates review status.

Uncertain significance

1 out of 6 submissions contributed to this 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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000009.11:g.(?_32453279)_(37785041_?)dup

Variation ID: 2422485 Accession: VCV002422485.14

Type and length

Duplication, 5,331,763 bp

Location

Cytogenetic: 9p21.1-13.2 9: 32453279-37785041 (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	Feb 13, 2023	Nov 11, 2023	Jul 12, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000009.11:g.(?_32453279)_(37785041_?)dup

Protein change

Other names

Canonical SPDI

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.
PAX5		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	421	581
B4GALT1		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	131	230
DNAI1		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	1022	1106
EXOSC3		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	289	382
FANCG		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	1351	1434
GALT		Gene associated with autosomal recessive phenotype	Not yet evaluated	GRCh38 GRCh37	815	1003
GBA2		Gene associated with autosomal recessive phenotype	Not yet evaluated	GRCh38 GRCh37	392	476
GRHPR		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	628	705
PIGO		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	1031	1111
RMRP		Gene associated with autosomal recessive phenotype	Not yet evaluated	GRCh38 GRCh37	811	892

There are 79 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37) and ClinGen Dosage Sensitivity Map.

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.
Acromesomelic dysplasia 1, Maroteaux type Tall stature-scoliosis-macrodactyly of the great toes syndrome	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV003109230.7
Frontotemporal dementia and/or amyotrophic lateral sclerosis 6 Inclusion body myopathy with Paget disease of bone and frontotemporal dementia	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV003109231.7
Primary ciliary dyskinesia	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV003119439.7
Arthrogryposis, distal, type 1A	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV003119438.7
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV003119437.7
not provided	Uncertain significance (1)	criteria provided, single submitter	Jul 12, 2022	RCV003154083.3

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.	Expand all rows Collapse all rows 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.
Uncertain significance (Jul 12, 2022) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	not provided	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003843944.1 First in ClinVar: Mar 26, 2023 Last updated: Mar 26, 2023	Comment: show A copy number gain of the genomic region encompassing the full coding sequence of the B4GALT1 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with B4GALT1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Jul 12, 2022) N Not contributing to aggregate classification	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003790761 appears to (...more) Source: NCBI	Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003790761.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Comment: show A copy number gain of the genomic region encompassing the full coding sequence of the GALT gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with GALT-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Jul 12, 2022) N Not contributing to aggregate classification	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003791333 appears to (...more) Source: NCBI	Arthrogryposis, distal, type 1A	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003791333.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Comment: show A copy number gain of the genomic region encompassing the full coding sequence of the TPM2 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with TPM2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Mar 27, 2022) N Not contributing to aggregate classification	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003792553 appears to (...more) Source: NCBI	Tall stature-scoliosis-macrodactyly of the great toes syndrome Acromesomelic dysplasia 1, Maroteaux type	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003792553.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Comment: show A copy number gain of the genomic region encompassing the full coding sequence of the NPR2 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with NPR2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Jul 12, 2022) N Not contributing to aggregate classification	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003791600 appears to (...more) Source: NCBI	Inclusion body myopathy with Paget disease of bone and frontotemporal dementia Frontotemporal dementia and/or amyotrophic lateral sclerosis 6	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003791600.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Comment: show A copy number gain of the genomic region encompassing the full coding sequence of the VCP gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with VCP-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Sep 29, 2022) N Not contributing to aggregate classification	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003792771 appears to (...more) Source: NCBI	Primary ciliary dyskinesia	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003792771.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Comment: show A copy number gain of the genomic region encompassing the full coding sequence of the DNAI1 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with DNAI1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more

Comment:

A copy number gain of the genomic region encompassing the full coding sequence of the B4GALT1 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with B4GALT1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Comment:

A copy number gain of the genomic region encompassing the full coding sequence of the GALT gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with GALT-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Comment:

A copy number gain of the genomic region encompassing the full coding sequence of the TPM2 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with TPM2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Comment:

A copy number gain of the genomic region encompassing the full coding sequence of the NPR2 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with NPR2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Comment:

A copy number gain of the genomic region encompassing the full coding sequence of the VCP gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with VCP-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Comment:

A copy number gain of the genomic region encompassing the full coding sequence of the DNAI1 gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with DNAI1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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 Nov 15, 2025

ClinVar Genomic variation as it relates to human health

NC_000009.11:g.(?_32453279)_(37785041_?)dup

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Citations for germline classification of this variant

Text-mined citations for this variant ...