NM_014324.6(AMACR):c.717G>T (p.Gln239His) AND not specified

Germline classification:: Benign (4 submissions)
Last evaluated:: May 31, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000116323.13

Allele description [Variation Report for NM_014324.6(AMACR):c.717G>T (p.Gln239His)]

NM_014324.6(AMACR):c.717G>T (p.Gln239His)

Genes:

C1QTNF3-AMACR:C1QTNF3-AMACR readthrough (NMD candidate) [Gene - HGNC]
AMACR:alpha-methylacyl-CoA racemase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p13.2

Genomic location:

Preferred name:

NM_014324.6(AMACR):c.717G>T (p.Gln239His)

Other names:

NM_001167595.1(AMACR):c.717G>T(p.Gln239His); NM_014324.5(AMACR):c.717G>T(p.Gln239His); NM_203382.2(AMACR):c.556G>T(p.Val186Phe)

HGVS:

NC_000005.10:g.33998663C>A
NG_016211.1:g.14453G>T
NM_001167595.2:c.717G>T
NM_014324.6:c.717G>TMANE SELECT
NM_203382.3:c.556G>T
NP_001161067.1:p.Gln239His
NP_055139.4:p.Gln239His
NP_976316.1:p.Val186Phe
NC_000005.9:g.33998768C>A
NM_014324.5:c.717G>T
NR_037951.1:n.1073G>T
Q9UHK6:p.Gln239His

Protein change:

Q239H

Links:

UniProtKB: Q9UHK6#VAR_055618; dbSNP: rs34677

NCBI 1000 Genomes Browser:

rs34677

Molecular consequence:

NM_001167595.2:c.717G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_014324.6:c.717G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_203382.3:c.556G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_037951.1:n.1073G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000150244	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000517699	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jan 21, 2016)	germline	clinical testing	Citation Link,
SCV000803560	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (May 31, 2018)	unknown	curation	PubMed (1) [See all records that cite this PMID]
SCV000861294	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Benign (May 17, 2018)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	14	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	curation
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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, SCV000150244.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV000517699.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From SIB Swiss Institute of Bioinformatics, SCV000803560.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)

Description

This variant is interpreted as a Benign - Stand Alone. The following ACMG Tag(s) were applied: BA1 => Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000861294.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	14	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		14	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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