VCV000154420.2 - ClinVar

GRCh38/hg38 10q11.22(chr10:46490281-47923579)x1

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.

Benign

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh38/hg38 10q11.22(chr10:46490281-47923579)x1

Variation ID: 154420 Accession: VCV000154420.2

Type and length

copy number loss, 1,433,299 bp

Location

Cytogenetic: 10q11.22 10: 46490281-47923579 (GRCh38) [ NCBI UCSC ] 10: 46951229-47410481 (GRCh37) [ NCBI UCSC ] 10: 46371235-46830487 (NCBI36) [ 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	Jul 10, 2015	Jul 10, 2015	Sep 21, 2012

HGVS

Nucleotide	Protein	Molecular consequence
NC_000010.11:g.(?_46490281)_(47923579_?)del
NC_000010.10:g.(?_46951229)_(47410481_?)del
NC_000010.9:g.(?_46371235)_(46830487_?)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

dbVar: nssv1601489 dbVar: nssv1601683 dbVar: nssv1602337 dbVar: nssv1602620 dbVar: nssv1603494 dbVar: nssv1603755 dbVar: nssv1603878 dbVar: nssv584005 dbVar: nssv584008 dbVar: nsv497879 VarSome

Comment on variant

When NCBI calculated the location of this variant on an assembly more recent than the one on which the variant was originally described, there were multiple placements. This suggests the variant falls within a region of the genome that changed significantly between assemblies. We present the highest-scoring placement here; however the variant's location should be interpreted with caution.

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.
GDF2		No evidence available	No evidence available	GRCh38 GRCh37	265	382
AGAP10	-	-	-	GRCh37	-	103
AGAP9	-	-	-	GRCh38 GRCh37	-	111
ANXA8		-	-	GRCh38 GRCh38 GRCh37	-	123
FAM245B	-	-	-	GRCh38	-	61
FAM25G	-	-	-	GRCh38 GRCh37	-	108
GDF10		-	-	GRCh38 GRCh37	45	160
GPRIN2		-	-	GRCh38 GRCh38 GRCh37	25	139
LINC02637	-	-	-	GRCh38	-	66
LINC03029	-	-	-	GRCh38	-	61

There are 18 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38 , GRCh37 , NCBI36) 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.
See cases	Benign (1)	no assertion criteria provided	Sep 21, 2012	RCV000142487.6

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.
Benign (Sep 21, 2012)	no assertion criteria provided Method: clinical testing	See cases Affected status: yes Allele origin: unknown	ISCA site 4 Additional submitter: International Standards For Cytogenomic Arrays Consortium (ISCA) Accession: SCV000174386.3 First in ClinVar: Sep 01, 2014 Last updated: Jul 10, 2015 Comment: Copy number variation identified through the course of routine clinical cytogenomic testing in postnatal populations, with clinical assertions as classified by the original submitter.	Publications: PubMed (1) PubMed: 20466091 Observation 1: Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Method: Microarray Observation 2: Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Method: Microarray Observation 3: Number of individuals with the variant: 1 Clinical Features: Abnormal facial shape (present) , High palate (present) , Long palpebral fissure (present) , Delayed speech and language development (present) , Ectropion of lower eyelids … (more) Abnormal facial shape (present) , High palate (present) , Long palpebral fissure (present) , Delayed speech and language development (present) , Ectropion of lower eyelids (present) , Delayed gross motor development (present) , Submucous cleft hard palate (present) , Short stature (present) , Prominent fingertip pads (present) , Delayed fine motor development (present) (less) Method: Microarray Observation 4: Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Method: Microarray Observation 5: Number of individuals with the variant: 1 Clinical Features: Autism (present) Method: Microarray Observation 6: Number of individuals with the variant: 1 Clinical Features: Cleft palate (present) , Cleft upper lip (present) Method: Microarray Observation 7: Number of individuals with the variant: 1 Clinical Features: Macrocephaly (present) , Global developmental delay (present) , Wide anterior fontanel (present) Method: Microarray Observation 8: Number of individuals with the variant: 1 Clinical Features: Developmental delay AND/OR other significant developmental or morphological phenotypes (present) Method: Microarray Observation 9: Number of individuals with the variant: 1 Clinical Features: Optic nerve hypoplasia (present) , Spastic diplegia (present) Method: Microarray

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 May 08, 2024

ClinVar Genomic variation as it relates to human health

GRCh38/hg38 10q11.22(chr10:46490281-47923579)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...