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NC_000007.14:g.156789600G>A AND Holoprosencephaly 3

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 18, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003619267.2

Allele description [Variation Report for NC_000007.14:g.156789600G>A]

NC_000007.14:g.156789600G>A

Genes:
SHH:sonic hedgehog signaling molecule [Gene - OMIM - HGNC]
LMBR1:limb development membrane protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q36.3
Genomic location:
Preferred name:
NC_000007.14:g.156789600G>A
HGVS:
  • NC_000007.14:g.156789600G>A
  • NG_009240.2:g.108609C>T
  • NM_001350953.2:c.423+6789C>T
  • NM_001350954.2:c.144+6789C>T
  • NM_001350955.2:c.-112+6789C>T
  • NM_001350956.2:c.-112+6789C>T
  • NM_001350957.2:c.54+6789C>T
  • NM_001350958.2:c.-112+6789C>T
  • NM_001363409.2:c.423+6789C>T
  • NM_001363410.2:c.423+6789C>T
  • NM_001363411.2:c.54+6789C>T
  • NM_001363412.2:c.360+6789C>T
  • NM_001363413.2:c.-112+6789C>T
  • NM_022458.4:c.423+6789C>TMANE SELECT
  • NC_000007.13:g.156582294G>A
Molecular consequence:
  • NM_001350953.2:c.423+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350954.2:c.144+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350955.2:c.-112+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350956.2:c.-112+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350957.2:c.54+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350958.2:c.-112+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363409.2:c.423+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363410.2:c.423+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363411.2:c.54+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363412.2:c.360+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363413.2:c.-112+6789C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_022458.4:c.423+6789C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Holoprosencephaly 3 (HPE3)
Identifiers:
MONDO: MONDO:0007733; MedGen: C1840529; Orphanet: 2162; OMIM: 142945

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004472418Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 18, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004472418.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. This variant has not been reported in the literature in individuals affected with SHH-related conditions. This variant is present in population databases (rs573676108, gnomAD 0.06%). This variant occurs in a non-coding region of the SHH gene. It does not change the encoded amino acid sequence of the SHH protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024