VCV000133306.10 - ClinVar

NM_022124.6(CDH23):c.9510+19_9510+25del

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.

(8)

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.

Conflicting classifications of pathogenicity
Uncertain significance(1); Benign(6)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_022124.6(CDH23):c.9510+19_9510+25del

Variation ID: 133306 Accession: VCV000133306.10

Type and length

Deletion, 7 bp

Location

Cytogenetic: 10q22.1 10: 71812625-71812631 (GRCh38) [ NCBI UCSC ] 10: 73572382-73572388 (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	Jun 9, 2014	Feb 14, 2024	Jan 31, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_022124.6:c.9510+19_9510+25del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_022124.6:c.9510+19_9510+25delGGCATCA MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NM_001171933.1:c.2790+19_2790+25del		intron variant
NM_001171934.1:c.2790+19_2790+25del		intron variant
NM_001171935.1:c.201+19_201+25del		intron variant
NM_001171936.1:c.201+19_201+25del		intron variant
NM_022124.3:c.9510+19_9510+25delGGCATCA
NM_022124.5:c.9510+16_9510+22delTCAGGCA
NC_000010.11:g.71812628_71812634del
NC_000010.10:g.73572385_73572391del
NG_008835.1:g.420682_420688del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000010.11:71812624:TCAGGCATCA:TCA

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.

0.02236 (TCA)

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA269907 dbSNP: rs149704197 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.
CDH23		-	-	GRCh38 GRCh37	4713	5559
PSAP		-	-	GRCh38 GRCh37	869	926

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.
Usher syndrome type 1D	Uncertain significance (1)	criteria provided, single submitter	-	RCV000119817.1
Metachromatic leukodystrophy	Benign (1)	criteria provided, single submitter	Jun 14, 2016	RCV000301614.5
Galactosylceramide beta-galactosidase deficiency	Benign (1)	criteria provided, single submitter	Jun 14, 2016	RCV000402429.5
Combined PSAP deficiency	Benign (1)	criteria provided, single submitter	Jun 14, 2016	RCV000337881.5
not specified	Benign (1)	criteria provided, single submitter	Mar 16, 2017	RCV000604131.1
Atypical Gaucher Disease	Benign (1)	criteria provided, single submitter	Jun 14, 2016	RCV000396275.5
not provided	Benign (1)	criteria provided, single submitter	Jan 31, 2024	RCV001523525.5
Usher syndrome type 1	Benign (1)	no assertion criteria provided	Sep 16, 2020	RCV001276931.1

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.
unknown (-)	criteria provided, single submitter (Submitter's publication) Method: not provided	not provided Affected status: not provided Allele origin: not provided	Molecular Genetics Laboratory; Baylor College of Medicine Accession: SCV000154743.2 First in ClinVar: Jun 09, 2014 Last updated: Jun 09, 2014	Publications: PubMed (1) PubMed: 25991456 Comment: Converted during submission to Uncertain significance.
Benign (Mar 16, 2017)	criteria provided, single submitter (GeneDx Variant Classification (06012015)) Method: clinical testing	not specified Affected status: yes Allele origin: germline	GeneDx Accession: SCV000731176.1 First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018	Comment: This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more) This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
Benign (Jun 14, 2016)	criteria provided, single submitter (ICSL Variant Classification 20161018) Method: clinical testing	Atypical Gaucher Disease Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000483094.2 First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016
Benign (Jun 14, 2016)	criteria provided, single submitter (ICSL Variant Classification 20161018) Method: clinical testing	Krabbe Disease Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000483091.2 First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016
Benign (Jun 14, 2016)	criteria provided, single submitter (ICSL Variant Classification 20161018) Method: clinical testing	Combined Saposin Deficiency Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000483093.2 First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016
Benign (Jun 14, 2016)	criteria provided, single submitter (ICSL Variant Classification 20161018) Method: clinical testing	Metachromatic Leukodystrophy Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000483092.2 First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016
Benign (Jan 31, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001733239.4 First in ClinVar: Jun 15, 2021 Last updated: Feb 14, 2024
Benign (Sep 16, 2020)	no assertion criteria provided Method: clinical testing	Usher syndrome type 1 Affected status: unknown Allele origin: germline	Natera, Inc. Accession: SCV001463588.1 First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021

Comment:

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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
DNA sequence analysis and genotype-phenotype assessment in 71 patients with syndromic hearing loss or auditory neuropathy.	Tang HY	BMJ open	2015	PMID: 25991456

Text-mined citations for rs149704197 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_022124.6(CDH23):c.9510+19_9510+25del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs149704197 ...