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NM_003383.5(VLDLR):c.1809C>T (p.Asn603=)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000378855.4
Variation ID:
378855
Description:
single nucleotide variant
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NM_003383.5(VLDLR):c.1809C>T (p.Asn603=)

Allele ID
370356
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p24.2
Genomic location
9: 2647579 (GRCh38) GRCh38 UCSC
9: 2647579 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.2647579C>T
NC_000009.12:g.2647579C>T
NM_003383.5:c.1809C>T MANE Select NP_003374.3:p.Asn603= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:2647578:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00089
The Genome Aggregation Database (gnomAD) 0.00092
1000 Genomes Project 0.00040
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00069
Links
ClinGen: CA4964937
dbSNP: rs6147
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jan 20, 2016 RCV000424647.1
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV000887422.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV001168789.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
VLDLR - - GRCh38
GRCh37
202 418

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 20, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000515253.4
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)
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001030978.2
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001331410.1
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)

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 rs6147...

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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