VCV001684630.2 - ClinVar

NC_000017.11:g.8117792_8126946del

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_000017.11:g.8117792_8126946del

Variation ID: 1684630 Accession: VCV001684630.2

Type and length

Deletion, 9,155 bp

Location

Cytogenetic: 17p13.1 17: 8117792-8126946 (GRCh38) [ NCBI UCSC ] 17: 8021110-8030264 (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	May 28, 2022	May 28, 2022	Aug 20, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NC_000017.11:g.8117792_8126946del
NC_000017.10:g.8021110_8030264del
NG_015807.1:g.2_6126del		genic upstream transcript variant
NG_015816.1:g.2147_10503del		genic upstream transcript variant

Protein change

Other names

del(17)(p13.1)

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.
ALOXE3		-	-	GRCh38 GRCh37	215	294
HES7		-	-	GRCh38 GRCh37	69	150
LOC126862485	-	-	-	GRCh38	-	29
LOC130060199	-	-	-	GRCh38	-	10
LOC130060200	-	-	-	GRCh38	-	9
LOC130060201	-	-	-	GRCh38	-	9
LOC130060202	-	-	-	GRCh38	-	9
LOC130060203	-	-	-	GRCh38	-	54
LOC130060204	-	-	-	GRCh38	-	9
LOC130060205	-	-	-	GRCh38	-	9

There are 6 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38 , GRCh37).

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.
Abnormal form of the vertebral bodies Brachycephaly Childhood-onset short-trunk short stature Congenital elevation of scapula Decreased body weight Delayed ability to stand Delayed ability to walk Delayed fine motor development Disproportionate short stature Failure to thrive in infancy Hemivertebrae Hypophosphatemia Intellectual disability Lumbar kyphoscoliosis Mild global developmental delay Mild malformation of cortical development Mitral regurgitation Neuropathic spinal arthropathy Progressive congenital scoliosis Progressive microcephaly Scoliosis Severe failure to thrive Short neck Short stature Skeletal dysplasia Tapered finger Thoracic kyphoscoliosis Thoracic scoliosis Thoracolumbar kyphoscoliosis Vertebral fusion	Pathogenic (1)	criteria provided, single submitter	Aug 20, 2021	RCV002247712.3

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.	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 (Aug 20, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Kidney disorder Brachycephaly Microcephaly Progressive microcephaly Facial asymmetry Short neck Congenital elevation of scapula Abnormality of the vertebral column Brachydactyly Tapered finger Intellectual disability Intellectual disability, mild Global developmental delay Failure to thrive Severe failure to thrive Failure to thrive in infancy Asymmetry of the thorax Mitral regurgitation Aortic regurgitation Acidosis Abnormal facial shape Hypophosphatemia Delayed gross motor development Scoliosis Skeletal dysplasia Kyphoscoliosis Hemivertebrae Thoracic scoliosis Thoracolumbar scoliosis Vertebral fusion Spinal rigidity Abnormal form of the vertebral bodies Butterfly vertebrae Thoracolumbar kyphoscoliosis Abnormal vertebral morphology Disproportionate short stature Disproportionate short-trunk short stature Short stature Decreased body weight Craniofacial asymmetry Lumbar kyphoscoliosis Secondary microcephaly Thoracic kyphoscoliosis Ichthyosis Spinal dysplasia Neuropathic spinal arthropathy Congenital kyphoscoliosis Progressive congenital scoliosis Neonatal short-trunk short stature Childhood-onset short-trunk short stature Asymmetric short stature Delayed fine motor development Hemifacial hypoplasia Mild global developmental delay Infancy onset short-trunk short stature Delayed ability to stand Delayed ability to sit Delayed ability to walk Mild malformation of cortical development Affected status: yes Allele origin: germline	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein Accession: SCV002515976.1 First in ClinVar: May 28, 2022 Last updated: May 28, 2022	Geographic origin: Brazil

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 Oct 13, 2024

ClinVar Genomic variation as it relates to human health

NC_000017.11:g.8117792_8126946del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...