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NM_001360.3(DHCR7):c.139C>T (p.Leu47=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Oct 22, 2021)
Last evaluated:
Jun 23, 2021
Accession:
VCV000283587.6
Variation ID:
283587
Description:
single nucleotide variant
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NM_001360.3(DHCR7):c.139C>T (p.Leu47=)

Allele ID
267824
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.4
Genomic location
11: 71444175 (GRCh38) GRCh38 UCSC
11: 71155221 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_340:g.9257C>T
LRG_340t1:c.139C>T LRG_340p1:p.Leu47=
NC_000011.10:g.71444175G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:71444174:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00031
The Genome Aggregation Database (gnomAD) 0.00027
Exome Aggregation Consortium (ExAC) 0.00014
The Genome Aggregation Database (gnomAD) 0.00025
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
Links
ClinGen: CA6162680
dbSNP: rs140721259
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 17, 2017 RCV000717988.1
Likely benign 1 criteria provided, single submitter May 23, 2020 RCV001483712.1
Likely benign 1 criteria provided, single submitter Jun 23, 2021 RCV001532990.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 18, 2021 RCV000279800.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
DHCR7 - - GRCh38
GRCh37
499 511

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 12, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000335785.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jan 17, 2017)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000848849.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Likely benign
(May 23, 2020)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: germline
Invitae
Accession: SCV001688114.1
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jun 23, 2021)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001748825.1
Submitted: (Jul 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: DHCR7 c.139C>T alters a conserved nucleotide resulting in a synonymous change. 4/4 computational tools predict no significant impact on normal splicing while predicting … (more)
Likely benign
(Jan 18, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001981889.1
Submitted: (Oct 22, 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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Title Author Journal Year Link
Mutational spectrum of Smith-Lemli-Opitz syndrome. Waterham HR American journal of medical genetics. Part C, Seminars in medical genetics 2012 PMID: 23042628
Smith-Lemli-Opitz syndrome and the DHCR7 gene. Jira PE Annals of human genetics 2003 PMID: 12914579
Mutations in the human DHCR7 gene. Witsch-Baumgartner M Human mutation 2001 PMID: 11241839
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=DHCR7 - - - -

Text-mined citations for rs140721259...

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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 Dec 04, 2021