NM_031448.6(C19orf12):c.69G>A (p.Ala23=) AND Neurodegeneration with brain iron accumulation 4

Germline classification:: Likely benign (4 submissions)
Last evaluated:: Jan 13, 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:: RCV000277296.13

Allele description [Variation Report for NM_031448.6(C19orf12):c.69G>A (p.Ala23=)]

NM_031448.6(C19orf12):c.69G>A (p.Ala23=)

Gene:

C19orf12:chromosome 19 open reading frame 12 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q12

Genomic location:

Preferred name:

NM_031448.6(C19orf12):c.69G>A (p.Ala23=)

HGVS:

NC_000019.10:g.29708345C>T
NG_031970.2:g.12445G>A
NM_001031726.4:c.69G>A
NM_001256046.3:c.69G>A
NM_001256047.2:c.69G>A
NM_001282929.1:c.-32-5368G>A
NM_001282930.3:c.-32-5368G>A
NM_001282931.3:c.-245G>A
NM_031448.6:c.69G>AMANE SELECT
NP_001026896.2:p.Ala34=
NP_001026896.3:p.Ala23=
NP_001242975.1:p.Ala23=
NP_001242976.1:p.Ala23=
NP_113636.2:p.Ala23=
NC_000019.9:g.30199252C>T
NM_001031726.3:c.102G>A
NM_031448.4:c.69G>A

Links:

dbSNP: rs201118405

NCBI 1000 Genomes Browser:

rs201118405

Molecular consequence:

NM_001282931.3:c.-245G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001282929.1:c.-32-5368G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001282930.3:c.-32-5368G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001031726.4:c.69G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001256046.3:c.69G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001256047.2:c.69G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_031448.6:c.69G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Neurodegeneration with brain iron accumulation 4 (NBIA4)
Synonyms:: MITOCHONDRIAL PROTEIN-ASSOCIATED NEURODEGENERATION
Identifiers:: MONDO: MONDO:0013674; MedGen: C3280371; Orphanet: 289560; OMIM: 614298

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Fabaceae ribosomal protein S16 (rpS16) gene, intron; chloroplast.
Fabaceae ribosomal protein S16 (rpS16) gene, intron; chloroplast.
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000411387	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV000733871	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000745296	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Jun 28, 2017)	germline	clinical testing	Citation Link,
SCV000745859	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided (ACGS Guidelines, 2013)	Likely benign (Sep 21, 2016)	germline	clinical testing	Citation Link

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Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000411387.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#	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 Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733871.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745296.1

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

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV000745859.1

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

Last Updated: Oct 20, 2024

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