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NM_001352514.2(HLCS):c.1074G>A (p.Thr358=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Sep 13, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000459945.7
Variation ID:
459945
Description:
single nucleotide variant
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NM_001352514.2(HLCS):c.1074G>A (p.Thr358=)

Allele ID
469617
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
21q22.13
Genomic location
21: 36936812 (GRCh38) GRCh38 UCSC
21: 38309112 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000021.8:g.38309112C>T
NC_000021.9:g.36936812C>T
NG_016193.2:g.58583G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000021.9:36936811:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00300 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00215
The Genome Aggregation Database (gnomAD) 0.00191
Exome Aggregation Consortium (ExAC) 0.00221
The Genome Aggregation Database (gnomAD), exomes 0.00229
Trans-Omics for Precision Medicine (TOPMed) 0.00247
1000 Genomes Project 0.00300
Links
ClinGen: CA10020639
dbSNP: rs116985497
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Mar 3, 2015 RCV001644630.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 8, 2020 RCV000551133.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HLCS - - GRCh38
GRCh37
504 570

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001856028.1
Submitted: (Sep 13, 2021)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Holocarboxylase synthetase deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001302181.1
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)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Holocarboxylase synthetase deficiency
Allele origin: germline
Invitae
Accession: SCV000631926.4
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 rs116985497...

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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 Sep 23, 2021