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NM_020549.5(CHAT):c.326C>T (p.Thr109Met) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Oct 4, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004023854.1

Allele description [Variation Report for NM_020549.5(CHAT):c.326C>T (p.Thr109Met)]

NM_020549.5(CHAT):c.326C>T (p.Thr109Met)

Gene:
CHAT:choline O-acetyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q11.23
Genomic location:
Preferred name:
NM_020549.5(CHAT):c.326C>T (p.Thr109Met)
HGVS:
  • NC_000010.11:g.49616541C>T
  • NG_011797.1:g.12447C>T
  • NM_001142929.2:c.-29C>T
  • NM_001142933.2:c.80C>T
  • NM_001142934.2:c.-29C>T
  • NM_020549.5:c.326C>TMANE SELECT
  • NM_020984.4:c.-29C>T
  • NM_020985.4:c.-29C>T
  • NM_020986.4:c.-29C>T
  • NP_001136405.2:p.Thr27Met
  • NP_065574.3:p.Thr109Met
  • NP_065574.4:p.Thr109Met
  • NC_000010.10:g.50824587C>T
  • NM_020549.4:c.326C>T
Protein change:
T109M
Links:
dbSNP: rs542610160
NCBI 1000 Genomes Browser:
rs542610160
Molecular consequence:
  • NM_001142929.2:c.-29C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001142934.2:c.-29C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_020984.4:c.-29C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_020985.4:c.-29C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_020986.4:c.-29C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001142933.2:c.80C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020549.5:c.326C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004924819Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Oct 4, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV004924819.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 7, 2025