NM_001360.3(DHCR7):c.99-4G>A AND not provided

Germline classification:: Benign/Likely benign (7 submissions)
Last evaluated:: Aug 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000428279.27

Allele description [Variation Report for NM_001360.3(DHCR7):c.99-4G>A]

NM_001360.3(DHCR7):c.99-4G>A

Genes:

NADSYN1:NAD synthetase 1 [Gene - OMIM - HGNC]
DHCR7:7-dehydrocholesterol reductase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.4

Genomic location:

Preferred name:

NM_001360.3(DHCR7):c.99-4G>A

HGVS:

NC_000011.10:g.71444219C>T
NG_012655.2:g.9213G>A
NM_001163817.2:c.99-4G>A
NM_001360.3:c.99-4G>AMANE SELECT
LRG_340t1:c.99-4G>A
LRG_340:g.9213G>A
NC_000011.9:g.71155265C>T
NM_001360.2:c.99-4G>A

Links:

dbSNP: rs140748737

NCBI 1000 Genomes Browser:

rs140748737

Molecular consequence:

NM_001163817.2:c.99-4G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001360.3:c.99-4G>A - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Human DNA sequence from clone RP11-5L19 on chromosome 1, complete sequence
Human DNA sequence from clone RP11-5L19 on chromosome 1, complete sequence
gi|18476593|emb|AL359373.21|

Nucleotide
ectodysplasin-A receptor-associated adapter protein isoform B, partial [Homo sap...
ectodysplasin-A receptor-associated adapter protein isoform B, partial [Homo sapiens]
gi|353453160|gb|AER00472.1|

Protein
Uncultured rumen protozoa clone GP26 18S ribosomal RNA gene, partial sequence
Uncultured rumen protozoa clone GP26 18S ribosomal RNA gene, partial sequence
gi|1449747709|gb|MF995618.1|

Nucleotide
Caenorhabditis elegans chromosome IV
Caenorhabditis elegans chromosome IV
gi|453232348|ref|NC_003282.8||gnl|A F_000002985.6|IV

Nucleotide
Nicoletella semolina 16S ribosomal RNA gene, partial sequence.
Nicoletella semolina 16S ribosomal RNA gene, partial sequence.
PopSet: 612134230

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000511366	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Sep 14, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000697861	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (May 2, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25040602, 23042628 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001135034	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001797508	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001848422	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Dec 17, 2018)	germline	clinical testing	Citation Link,
SCV001929097	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002585336	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Aug 1, 2024)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	29	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Characterization of large deletions in the DHCR7 gene.

Lanthaler B, Hinderhofer K, Maas B, Haas D, Sawyer H, Burton-Jones S, Carter K, Suri M, Witsch-Baumgartner M.

Clin Genet. 2015 Aug;88(2):149-54. doi: 10.1111/cge.12454. Epub 2014 Oct 21.

PubMed [citation]

PMID:: 25040602

See all PubMed Citations (3)

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000511366.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Converted during submission to Likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.010396	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697861.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: The DHCR7 c.99-4G>A variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 628/37018 control chromosomes (8 homozygotes) at a frequency of 0.0169647, which is approximately 4 times the estimated maximal expected allele frequency of a pathogenic DHCR7 variant (0.0043301), suggesting this variant is likely a benign polymorphism. The variant of interest has been reported in affected individuals without strong evidence for causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mendelics, SCV001135034.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001797508.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001848422.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is associated with the following publications: (PMID: 25040602, 23042628)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001929097.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002585336.15

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	29	not provided	not provided	clinical testing	not provided

Description

DHCR7: BP4, BS1, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		29	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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