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NM_020549.5(CHAT):c.1674C>T (p.Ser558=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 25, 2020
Accession:
VCV000128720.4
Variation ID:
128720
Description:
single nucleotide variant
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NM_020549.5(CHAT):c.1674C>T (p.Ser558=)

Allele ID
134169
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q11.23
Genomic location
10: 49655134 (GRCh38) GRCh38 UCSC
10: 50863180 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.50863180C>T
NM_020549.4:c.1674C>T NP_065574.3:p.Ser558= synonymous
NC_000010.10:g.50863180C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:49655133:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.02436 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.02212
1000 Genomes Project 0.02436
Exome Aggregation Consortium (ExAC) 0.00653
The Genome Aggregation Database (gnomAD) 0.01912
The Genome Aggregation Database (gnomAD), exomes 0.00541
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02376
Links
ClinGen: CA152343
dbSNP: rs7073028
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Dec 31, 2016 RCV000116693.3
Benign 1 criteria provided, single submitter Nov 25, 2020 RCV000546596.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CHAT - - GRCh38
GRCh37
401 499

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Aug 15, 2013)
criteria provided, single submitter
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000150662.1
Submitted: (Apr 30, 2014)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000313621.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Dec 31, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000729901.1
Submitted: (Mar 26, 2018)
Evidence details
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)
Benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Familial infantile myasthenia
Allele origin: germline
Invitae
Accession: SCV000634121.5
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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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 this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs7073028...

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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 Oct 24, 2021