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NM_003383.5(VLDLR):c.1458C>T (p.Ala486=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
Jan 13, 2018
Accession:
VCV000130703.2
Variation ID:
130703
Description:
single nucleotide variant
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NM_003383.5(VLDLR):c.1458C>T (p.Ala486=)

Allele ID
136149
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p24.2
Genomic location
9: 2645719 (GRCh38) GRCh38 UCSC
9: 2645719 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.2645719C>T
NC_000009.12:g.2645719C>T
NM_003383.5:c.1458C>T MANE Select NP_003374.3:p.Ala486= synonymous
... more HGVS
Protein change
-
Other names
p.A486A:GCC>GCT
Canonical SPDI
NC_000009.12:2645718:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.04752 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.04085
Exome Aggregation Consortium (ExAC) 0.01502
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.04652
The Genome Aggregation Database (gnomAD), exomes 0.01302
1000 Genomes Project 0.04752
Trans-Omics for Precision Medicine (TOPMed) 0.04546
Links
ClinGen: CA155912
dbSNP: rs6143
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, single submitter Mar 21, 2014 RCV000118817.5
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000370518.1
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV001168017.1
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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
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Cerebellar Hypoplasia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000479349.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Mar 21, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000169804.9
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
(Jan 13, 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: SCV001330570.1
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)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000153464.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (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 rs6143...

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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