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NM_000384.3(APOB):c.9477G>A (p.Lys3159=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 30, 2020
Accession:
VCV000334113.5
Variation ID:
334113
Description:
single nucleotide variant
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NM_000384.3(APOB):c.9477G>A (p.Lys3159=)

Allele ID
284434
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p24.1
Genomic location
2: 21007391 (GRCh38) GRCh38 UCSC
2: 21230263 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.12:g.21007391C>T
NC_000002.11:g.21230263C>T
NM_000384.3:c.9477G>A MANE Select NP_000375.3:p.Lys3159= synonymous
NG_011793.1:g.41683G>A
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:21007390:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00459 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00193
Trans-Omics for Precision Medicine (TOPMed) 0.00181
1000 Genomes Project 0.00459
The Genome Aggregation Database (gnomAD), exomes 0.00205
The Genome Aggregation Database (gnomAD) 0.00153
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA066576
dbSNP: rs13306196
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 2, 2018 RCV000292000.4
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000377029.2
Benign 1 criteria provided, single submitter Nov 30, 2020 RCV000532658.5
Likely benign 1 criteria provided, single submitter Oct 2, 2017 RCV000610530.1
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001094630.1
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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
2194 2311

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Nov 06, 2017)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia
Allele origin: germline
Color Health, Inc
Accession: SCV000687275.1
Submitted: (Dec 21, 2017)
Evidence details
Likely benign
(Oct 02, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000731085.1
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 1
(Autosomal dominant inheritance)
Allele origin: germline
Robarts Research Institute,Western University
Accession: SCV000782897.1
Submitted: (Apr 09, 2018)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hypobetalipoproteinemia, familial, 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000427001.3
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
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hypercholesterolemia 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000427002.3
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)
Benign
(Nov 30, 2020)
criteria provided, single submitter
Method: clinical testing
Hypobetalipoproteinemia, familial, 1
Familial hypercholesterolemia 2
Allele origin: germline
Invitae
Accession: SCV000659307.5
Submitted: (Jan 07, 2021)
Evidence details

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs13306196...

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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 Jun 14, 2021