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NM_000384.2(APOB):c.13451C>T (p.Thr4484Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(5);Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
10 (Most recent: Sep 19, 2018)
Last evaluated:
Jun 13, 2018
Accession:
VCV000255978.1
Variation ID:
255978
Description:
single nucleotide variant
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NM_000384.2(APOB):c.13451C>T (p.Thr4484Met)

Allele ID
250516
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p24.1
Genomic location
2: 21001971 (GRCh38) GRCh38 UCSC
2: 21224843 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.21224843G>A
NC_000002.12:g.21001971G>A
NM_000384.2:c.13451C>T NP_000375.2:p.Thr4484Met missense
NG_011793.1:g.47103C>T
Protein change
T4484M
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.03834 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.01124
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.03744
1000 Genomes Project 0.03834
Trans-Omics for Precision Medicine (TOPMed) 0.03670
The Genome Aggregation Database (gnomAD) 0.03344
Links
dbSNP: rs12713450
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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 Jun 13, 2018 RCV000249837.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000373894.1
Benign 1 criteria provided, single submitter Aug 21, 2017 RCV000477618.2
Conflicting interpretations of pathogenicity 5 criteria provided, conflicting interpretations Jan 2, 2018 RCV000256275.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
APOB No evidence available No evidence available GRCh38
GRCh37
895 961

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics
Accession: SCV000303932.1
Submitted: (Apr 28, 2016)
Evidence details
Uncertain significance
(Mar 01, 2016)
criteria provided, single submitter
Method: research
Familial hypercholesterolemias
Allele origin: germline
Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge
Accession: SCV000322866.1
Submitted: (Oct 14, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Familial Hypobetalipoproteinemia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000426892.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Familial Hypercholesterolemia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000426891.2
Submitted: (Oct 18, 2016)
Evidence details
Uncertain significance
(Mar 01, 2016)
criteria provided, single submitter
Method: research
Familial hypercholesterolemias
Allele origin: germline
Laboratory of Genetics and Molecular Cardiology,University of São Paulo
Study: HipercolBrasil
Accession: SCV000588468.1
Submitted: (Aug 04, 2017)
Evidence details
Benign
(Aug 21, 2017)
criteria provided, single submitter
Method: clinical testing
Hypobetalipoproteinemia, familial, 1
Hypercholesterolemia, autosomal dominant, type B
Allele origin: germline
Invitae
Accession: SCV000554814.2
Submitted: (Oct 05, 2017)
Evidence details
Benign
(Jun 27, 2017)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemias
Allele origin: germline
Color
Accession: SCV000687208.1
Submitted: (Dec 21, 2017)
Evidence details
Benign
(Jan 09, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000521120.4
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)
Likely benign
(Jan 02, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia
(Autosomal dominant inheritance)
Allele origin: germline
Robarts Research Institute,Western University
Accession: SCV000782813.1
Submitted: (Apr 09, 2018)
Evidence details
Benign
(Jun 13, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000861839.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/em...

Citations for this variant

Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=APOB - - - -

Record last updated Jun 26, 2019