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NM_004656.4(BAP1):c.1890G>A (p.Lys630=) AND BAP1-related tumor predisposition syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 11, 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:
RCV002585017.3

Allele description [Variation Report for NM_004656.4(BAP1):c.1890G>A (p.Lys630=)]

NM_004656.4(BAP1):c.1890G>A (p.Lys630=)

Gene:
BAP1:BRCA1 associated deubiquitinase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.1
Genomic location:
Preferred name:
NM_004656.4(BAP1):c.1890G>A (p.Lys630=)
HGVS:
  • NC_000003.12:g.52403138C>T
  • NG_031859.1:g.11856G>A
  • NM_001410772.1:c.1836G>A
  • NM_004656.4:c.1890G>AMANE SELECT
  • NP_001397701.1:p.Lys612=
  • NP_004647.1:p.Lys630=
  • NP_004647.1:p.Lys630=
  • LRG_529t1:c.1890G>A
  • LRG_529:g.11856G>A
  • LRG_529p1:p.Lys630=
  • NC_000003.11:g.52437154C>T
  • NM_004656.2:c.1890G>A
Molecular consequence:
  • NM_001410772.1:c.1836G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004656.4:c.1890G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
BAP1-related tumor predisposition syndrome (TPDS1)
Synonyms:
Tumor predisposition syndrome; Tumor susceptibility linked to germline BAP1 mutations; BAP1 tumor predisposition syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0013692; MedGen: C3280492; Orphanet: 289539; OMIM: 614327

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003489248Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 11, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003489248.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with BAP1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects codon 630 of the BAP1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the BAP1 protein. This variant also falls at the last nucleotide of exon 14, which is part of the consensus splice site for this exon.

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

Last Updated: Sep 29, 2024