VCV002504286.3 - ClinVar

NM_000899.5(KITLG):c.715-2A>G

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.

(3)

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
Likely pathogenic(1); Uncertain significance(2)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000899.5(KITLG):c.715-2A>G

Variation ID: 2504286 Accession: VCV002504286.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 12q21.32 12: 88506380 (GRCh38) [ NCBI UCSC ] 12: 88900157 (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 10, 2023	Oct 8, 2024	May 7, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000899.5:c.715-2A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor
NM_003994.6:c.631-2A>G		splice acceptor
NC_000012.12:g.88506380T>C
NC_000012.11:g.88900157T>C
NG_012098.2:g.79082A>G
LRG_1379:g.79082A>G
LRG_1379t1:c.715-2A>G

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000012.12:88506379:T:C

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.
KITLG		-	-	GRCh38 GRCh37	103	115

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.
Autosomal dominant nonsyndromic hearing loss 69	Likely pathogenic (1)	criteria provided, single submitter	Sep 9, 2020	RCV003231747.2
not provided	Uncertain significance (2)	criteria provided, multiple submitters, no conflicts	May 7, 2024	RCV003231746.4

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.
Likely pathogenic (Sep 09, 2020)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Autosomal dominant nonsyndromic hearing loss 69 (Autosomal dominant inheritance) Affected status: yes Allele origin: paternal	Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen Accession: SCV003926657.1 First in ClinVar: Jun 10, 2023 Last updated: Jun 10, 2023	Comment: The detected alteration is reported in the dbSNP database (dbSNP151) as rs768146588. It has been detected in the general population at a frequency of 0.0070845% … (more) The detected alteration is reported in the dbSNP database (dbSNP151) as rs768146588. It has been detected in the general population at a frequency of 0.0070845% (20/282286) (gnomAD/Genomes+Exomes v2.1.1). The variant has not yet been described in the ClinVar database. (as of 04/19/2023) The variant has been reported once in the literature in a patient with DFNA694. Bioinformatic prediction tools predict a negative effect on the canonical acceptor splice site of exon 8 (SSF, MaxENT). Splice variants of the canonical ± 1 or 2 splice site in a gene (and inheritance) matching the phenotype, where loss-of-function alterations are a known pathomechanism, are highly likely to have pathogenetic relevance. Based on the current state of knowledge, the variant has been classified as "likely pathogenic". (less) Sex: male
Uncertain significance (Aug 31, 2023)	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: SCV004537715.1 First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024	Publications: PubMed (2) PubMed: 16199547‚ 33229591 Comment: This sequence change affects an acceptor splice site in intron 7 of the KITLG gene. It is expected to disrupt RNA splicing. Variants that disrupt … (more) This sequence change affects an acceptor splice site in intron 7 of the KITLG gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), however the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in KITLG cause disease. This variant is present in population databases (rs768146588, gnomAD 0.02%). Disruption of this splice site has been observed in individual(s) with deafness (PMID: 33229591). ClinVar contains an entry for this variant (Variation ID: 2504286). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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)
Uncertain significance (May 07, 2024)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV003929780.2 First in ClinVar: Jun 10, 2023 Last updated: Oct 08, 2024	Comment: Reported in a patient with age-related hearing loss in published literature (PMID: 33229591); Canonical splice site variant in a gene or region of a gene … (more) Reported in a patient with age-related hearing loss in published literature (PMID: 33229591); Canonical splice site variant in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; This variant is associated with the following publications: (PMID: 33229591) (less)

Comment:

The detected alteration is reported in the dbSNP database (dbSNP151) as rs768146588. It has been detected in the general population at a frequency of 0.0070845% (20/282286) (gnomAD/Genomes+Exomes v2.1.1). The variant has not yet been described in the ClinVar database. (as of 04/19/2023) The variant has been reported once in the literature in a patient with DFNA694. Bioinformatic prediction tools predict a negative effect on the canonical acceptor splice site of exon 8 (SSF, MaxENT). Splice variants of the canonical ± 1 or 2 splice site in a gene (and inheritance) matching the phenotype, where loss-of-function alterations are a known pathomechanism, are highly likely to have pathogenetic relevance. Based on the current state of knowledge, the variant has been classified as "likely pathogenic".

Comment:

This sequence change affects an acceptor splice site in intron 7 of the KITLG gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), however the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in KITLG cause disease. This variant is present in population databases (rs768146588, gnomAD 0.02%). Disruption of this splice site has been observed in individual(s) with deafness (PMID: 33229591). ClinVar contains an entry for this variant (Variation ID: 2504286). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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:

Reported in a patient with age-related hearing loss in published literature (PMID: 33229591); Canonical splice site variant in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; This variant is associated with the following publications: (PMID: 33229591)

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
Ultrarare heterozygous pathogenic variants of genes causing dominant forms of early-onset deafness underlie severe presbycusis.	Boucher S	Proceedings of the National Academy of Sciences of the United States of America	2020	PMID: 33229591
Splicing in action: assessing disease causing sequence changes.	Baralle D	Journal of medical genetics	2005	PMID: 16199547

Text-mined citations for this variant ...

Record last updated Oct 08, 2024

ClinVar Genomic variation as it relates to human health

NM_000899.5(KITLG):c.715-2A>G

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...