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NM_004656.4(BAP1):c.1890G>C (p.Lys630Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 3, 2021
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:
RCV002408021.2

Allele description [Variation Report for NM_004656.4(BAP1):c.1890G>C (p.Lys630Asn)]

NM_004656.4(BAP1):c.1890G>C (p.Lys630Asn)

Gene:
BAP1:BRCA1 associated protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.1
Genomic location:
Preferred name:
NM_004656.4(BAP1):c.1890G>C (p.Lys630Asn)
HGVS:
  • NC_000003.12:g.52403138C>G
  • NG_031859.1:g.11856G>C
  • NM_001410772.1:c.1836G>C
  • NM_004656.4:c.1890G>CMANE SELECT
  • NP_001397701.1:p.Lys612Asn
  • NP_004647.1:p.Lys630Asn
  • NP_004647.1:p.Lys630Asn
  • LRG_529t1:c.1890G>C
  • LRG_529:g.11856G>C
  • LRG_529p1:p.Lys630Asn
  • NC_000003.11:g.52437154C>G
  • NM_004656.2:c.1890G>C
Protein change:
K612N
Molecular consequence:
  • NM_001410772.1:c.1836G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004656.4:c.1890G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002719163Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Jun 3, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002719163.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1890G>C variant (also known as p.K630N), located in coding exon 14 of the BAP1 gene, results from a G to C substitution at nucleotide position 1890. The amino acid change results in lysine to asparagine at codon 630, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 14, which makes it likely to have some effect on normal mRNA splicing. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site; however, direct evidence is unavailable. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: May 1, 2024