NM_000390.4(CHM):c.1350-15_1350-10del AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 4, 2022
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:: RCV001226392.5

Allele description [Variation Report for NM_000390.4(CHM):c.1350-15_1350-10del]

NM_000390.4(CHM):c.1350-15_1350-10del

Gene:

CHM:CHM Rab escort protein [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq21.2

Genomic location:

Preferred name:

NM_000390.4(CHM):c.1350-15_1350-10del

HGVS:

NC_000023.11:g.85900719_85900724del
NG_009874.2:g.151839_151844del
NM_000390.4:c.1350-15_1350-10delMANE SELECT
NM_001320959.1:c.906-15_906-10del
NM_001362517.1:c.906-15_906-10del
NM_001362518.2:c.906-15_906-10del
NM_001362519.1:c.906-15_906-10del
LRG_699t1:c.1350-15_1350-10del
LRG_699:g.151839_151844del
NC_000023.10:g.85155724_85155729del
NM_000390.2:c.1350-15_1350-10del

Links:

dbSNP: rs1926214121

NCBI 1000 Genomes Browser:

rs1926214121

Molecular consequence:

NM_000390.4:c.1350-15_1350-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001320959.1:c.906-15_906-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001362517.1:c.906-15_906-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001362518.2:c.906-15_906-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001362519.1:c.906-15_906-10del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001398704	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 4, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001398704

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 4, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001398704.5

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

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 954013). This variant has not been reported in the literature in individuals affected with CHM-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 10 of the CHM gene. It does not directly change the encoded amino acid sequence of the CHM protein. 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.

#	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

Last Updated: Feb 20, 2024

ClinVar

Relating variation to medicine