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NM_001360.3(DHCR7):c.70G>T (p.Ala24Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Aug 10, 2021)
Last evaluated:
Dec 29, 2020
Accession:
VCV000093723.10
Variation ID:
93723
Description:
single nucleotide variant
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NM_001360.3(DHCR7):c.70G>T (p.Ala24Ser)

Allele ID
99626
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.4
Genomic location
11: 71444883 (GRCh38) GRCh38 UCSC
11: 71155929 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001360.3:c.70G>T MANE Select NP_001351.2:p.Ala24Ser missense
LRG_340:g.8549G>T
LRG_340t1:c.70G>T LRG_340p1:p.Ala24Ser
... more HGVS
Protein change
A24S
Other names
-
Canonical SPDI
NC_000011.10:71444882:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (A)

Allele frequency
1000 Genomes Project 0.00200
Trans-Omics for Precision Medicine (TOPMed) 0.00260
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00285
Links
ClinGen: CA147253
dbSNP: rs146867923
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 Dec 1, 2016 RCV000079659.6
Likely benign 1 criteria provided, single submitter Jul 31, 2018 RCV000717684.1
Likely benign 1 criteria provided, single submitter Dec 29, 2020 RCV001554963.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 1, 2020 RCV000380891.4
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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
Benign
(Mar 18, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000111542.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 01, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000594363.1
Submitted: (Jul 05, 2017)
Evidence details
Uncertain significance
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000373930.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Jul 31, 2018)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000848540.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign) ;Sub-population frequency in support of benign classification (not ava blue, manual h-w)
Likely benign
(Dec 01, 2020)
criteria provided, single submitter
Method: clinical testing
Smith-Lemli-Opitz syndrome
Allele origin: germline
Invitae
Accession: SCV001021812.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Dec 29, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001776304.1
Submitted: (Aug 10, 2021)
Evidence details
Comment:
The majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014); In silico analysis, which includes protein predictors and evolutionary conservation, … (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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=DHCR7 - - - -

Text-mined citations for rs146867923...

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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 Nov 20, 2021