NM_020549.4(CHAT):c.1674C>T (p.Ser558=) AND not specified

Clinical significance:Benign (Last evaluated: Dec 31, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000116693.3

Allele description [Variation Report for NM_020549.4(CHAT):c.1674C>T (p.Ser558=)]

NM_020549.4(CHAT):c.1674C>T (p.Ser558=)

Gene:
CHAT:choline O-acetyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q11.23
Genomic location:
Preferred name:
NM_020549.4(CHAT):c.1674C>T (p.Ser558=)
HGVS:
  • NC_000010.11:g.49655134C>T
  • NG_011797.1:g.51040C>T
  • NM_001142929.1:c.1320C>T
  • NM_001142933.1:c.1428C>T
  • NM_001142934.1:c.1320C>T
  • NM_020549.4:c.1674C>T
  • NM_020984.3:c.1320C>T
  • NM_020985.3:c.1320C>T
  • NM_020986.3:c.1320C>T
  • NP_001136401.1:p.Ser440=
  • NP_001136405.1:p.Ser476=
  • NP_001136406.1:p.Ser440=
  • NP_065574.3:p.Ser558=
  • NP_066264.3:p.Ser440=
  • NP_066265.3:p.Ser440=
  • NP_066266.3:p.Ser440=
  • NC_000010.10:g.50863180C>T
Links:
dbSNP: rs7073028
NCBI 1000 Genomes Browser:
rs7073028
Molecular consequence:
  • NM_001142929.1:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001142933.1:c.1428C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001142934.1:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_020549.4:c.1674C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_020984.3:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_020985.3:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_020986.3:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000150662Genetic Services Laboratory, University of Chicagocriteria provided, single submitter
Benign
(Aug 15, 2013)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000313621PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000729901GeneDxcriteria provided, single submitter
Benign
(Dec 31, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
germlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]
PMID:
18414213

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000150662.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From PreventionGenetics,PreventionGenetics, SCV000313621.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV000729901.1

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

Description

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.

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

Last Updated: Jun 23, 2021

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