VCV001705068.2 - ClinVar

NM_020549.5(CHAT):c.1468_1470delinsC (p.Glu490fs)

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.

(2)

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.

Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_020549.5(CHAT):c.1468_1470delinsC (p.Glu490fs)

Variation ID: 1705068 Accession: VCV001705068.2

Type and length

Indel, 3 bp

Location

Cytogenetic: 10q11.23 10: 49649593-49649595 (GRCh38) [ NCBI UCSC ] 10: 50857639-50857641 (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	Sep 17, 2022	Dec 30, 2023	Feb 5, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_020549.5:c.1468_1470delinsC MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_065574.4:p.Glu490fs	frameshift
NM_001142929.2:c.1114_1116delinsC	NP_001136401.2:p.Glu372fs	frameshift
NM_001142933.2:c.1222_1224delinsC	NP_001136405.2:p.Glu408fs	frameshift
NM_001142934.2:c.1114_1116delinsC	NP_001136406.2:p.Glu372fs	frameshift
NM_020549.4:c.1468_1470delGAAinsC	NP_065574.3:p.Glu490Hisfs	frameshift
NM_020984.4:c.1114_1116delinsC	NP_066264.4:p.Glu372fs	frameshift
NM_020985.4:c.1114_1116delinsC	NP_066265.4:p.Glu372fs	frameshift
NM_020986.4:c.1114_1116delinsC	NP_066266.4:p.Glu372fs	frameshift
NC_000010.11:g.49649593_49649595delinsC
NC_000010.10:g.50857639_50857641delinsC
NG_011797.1:g.45499_45501delinsC

... more HGVS ... less HGVS

Protein change

E372fs, E408fs, E490fs

Other names

Canonical SPDI

NC_000010.11:49649592:GAA: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.
CHAT		-	-	GRCh38 GRCh37	971	1309

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.
Congenital myasthenic syndrome	Likely pathogenic (1)	criteria provided, single submitter	Aug 10, 2022	RCV002283393.1
Familial infantile myasthenia	Likely pathogenic (1)	criteria provided, single submitter	Feb 5, 2023	RCV003471308.1

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.
Likely pathogenic (Aug 10, 2022)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	Congenital myasthenic syndrome Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV002571935.1 First in ClinVar: Sep 17, 2022 Last updated: Sep 17, 2022	Comment: Variant summary: CHAT c.1468_1470delinsC (p.Glu490HisfsX20) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more) Variant summary: CHAT c.1468_1470delinsC (p.Glu490HisfsX20) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been reported in affected individuals (HGMD). The variant was absent in 249678 control chromosomes (gnomAD). To our knowledge, no occurrence of c.1468_1470delinsC in individuals affected with Congenital Myasthenic Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic. (less)
Likely pathogenic (Feb 05, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Familial infantile myasthenia Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV004215827.1 First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023

Comment:

Variant summary: CHAT c.1468_1470delinsC (p.Glu490HisfsX20) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been reported in affected individuals (HGMD). The variant was absent in 249678 control chromosomes (gnomAD). To our knowledge, no occurrence of c.1468_1470delinsC in individuals affected with Congenital Myasthenic Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

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 Dec 30, 2023

ClinVar Genomic variation as it relates to human health

NM_020549.5(CHAT):c.1468_1470delinsC (p.Glu490fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...