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NM_006949.4(STXBP2):c.1538+12G>C AND Familial hemophagocytic lymphohistiocytosis 5

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Mar 7, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV003138854.4

Allele description [Variation Report for NM_006949.4(STXBP2):c.1538+12G>C]

NM_006949.4(STXBP2):c.1538+12G>C

Gene:
STXBP2:syntaxin binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_006949.4(STXBP2):c.1538+12G>C
HGVS:
  • NC_000019.10:g.7647259G>C
  • NG_016709.1:g.15155G>C
  • NM_001127396.3:c.1529+12G>C
  • NM_001272034.2:c.1571+12G>C
  • NM_006949.4:c.1538+12G>CMANE SELECT
  • LRG_165:g.15155G>C
  • NC_000019.9:g.7712145G>C
  • NM_006949.3:c.1538+12G>C
Molecular consequence:
  • NM_001127396.3:c.1529+12G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001272034.2:c.1571+12G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006949.4:c.1538+12G>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Familial hemophagocytic lymphohistiocytosis 5
Identifiers:
MONDO: MONDO:0013135; MedGen: C2751293; Orphanet: 540; OMIM: 613101

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003818132Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Mar 23, 2020)
germlineclinical testing

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

SCV004433115Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Mar 7, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

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 Revvity Omics, Revvity, SCV003818132.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV004433115.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 16, 2024