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NM_000384.3(APOB):c.7612C>T (p.Leu2538=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 2, 2021)
Last evaluated:
Jan 7, 2021
Accession:
VCV000255988.10
Variation ID:
255988
Description:
single nucleotide variant
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NM_000384.3(APOB):c.7612C>T (p.Leu2538=)

Allele ID
250525
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p24.1
Genomic location
2: 21009256 (GRCh38) GRCh38 UCSC
2: 21232128 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.21232128G>A
NC_000002.12:g.21009256G>A
NG_011793.1:g.39818C>T
NM_000384.3:c.7612C>T MANE Select NP_000375.3:p.Leu2538= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:21009255:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD) 0.00086
Trans-Omics for Precision Medicine (TOPMed) 0.00106
The Genome Aggregation Database (gnomAD), exomes 0.00130
Trans-Omics for Precision Medicine (TOPMed) 0.00108
The Genome Aggregation Database (gnomAD) 0.00108
Exome Aggregation Consortium (ExAC) 0.00151
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00192
Links
ClinGen: CA064592
dbSNP: rs72653093
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 2, 2018 RCV000309008.3
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 7, 2021 RCV000473010.8
Likely benign 1 criteria provided, single submitter - RCV000254500.1
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000363741.2
Benign 1 criteria provided, single submitter Jun 29, 2018 RCV000771105.1
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV001094633.1
Benign 1 criteria provided, single submitter Dec 2, 2020 RCV001083127.2
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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 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2221 2338

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303950.1
Submitted: (Apr 28, 2016)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Hypobetalipoproteinemia, familial, 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000427035.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000427034.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Likely benign
(Sep 03, 2017)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia
Allele origin: germline
Color Health, Inc
Accession: SCV000687263.1
Submitted: (Dec 21, 2017)
Evidence details
Likely benign
(Jan 02, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia 1
(Autosomal dominant inheritance)
Allele origin: germline
Robarts Research Institute,Western University
Accession: SCV000782882.1
Submitted: (Apr 09, 2018)
Evidence details
Benign
(Jun 29, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemias
Allele origin: germline
Color Health, Inc
Accession: SCV000902774.1
Submitted: (Nov 06, 2018)
Evidence details
Benign
(May 13, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001133418.2
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (1)
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
Hypobetalipoproteinemia, familial, 1
Familial hypercholesterolemia 2
Allele origin: germline
Invitae
Accession: SCV000554845.6
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 07, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001825212.1
Submitted: (Sep 02, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 31150472, 30333156)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Evaluation of Recipients of Positive and Negative Secondary Findings Evaluations in a Hybrid CLIA-Research Sequencing Pilot. Sapp JC American journal of human genetics 2018 PMID: 30122538

Text-mined citations for rs72653093...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021