NM_031885.5(BBS2):c.1398-2A>G AND Bardet-Biedl syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 21, 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:: RCV001220353.5

Allele description [Variation Report for NM_031885.5(BBS2):c.1398-2A>G]

NM_031885.5(BBS2):c.1398-2A>G

Gene:

BBS2:Bardet-Biedl syndrome 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q13

Genomic location:

Preferred name:

NM_031885.5(BBS2):c.1398-2A>G

HGVS:

NC_000016.10:g.56499909T>C
NG_009312.2:g.25116A>G
NM_001377456.1:c.1398-2A>G
NM_031885.5:c.1398-2A>GMANE SELECT
NC_000016.9:g.56533821T>C
NM_031885.3:c.1398-2A>G

Links:

dbSNP: rs767609303

NCBI 1000 Genomes Browser:

rs767609303

Molecular consequence:

NM_001377456.1:c.1398-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_031885.5:c.1398-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Bardet-Biedl syndrome (BBS)
Identifiers:: MONDO: MONDO:0015229; MedGen: C0752166; Orphanet: 110; OMIM: PS209900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001392336	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jul 21, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 16199547, 11285252, 20177705, 24608809, 26518167, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001392336

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jul 21, 2023)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Positional cloning of a novel gene on chromosome 16q causing Bardet-Biedl syndrome (BBS2).

Nishimura DY, Searby CC, Carmi R, Elbedour K, Van Maldergem L, Fulton AB, Lam BL, Powell BR, Swiderski RE, Bugge KE, Haider NB, Kwitek-Black AE, Ying L, Duhl DM, Gorman SW, Heon E, Iannaccone A, Bonneau D, Biesecker LG, Jacobson SG, Stone EM, Sheffield VC.

Hum Mol Genet. 2001 Apr 1;10(8):865-74.

PubMed [citation]

PMID:: 11285252

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001392336.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. 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: 948986). This variant has not been reported in the literature in individuals affected with BBS2-related conditions. This variant is present in population databases (rs767609303, gnomAD 0.0009%). This sequence change affects an acceptor splice site in intron 11 of the BBS2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BBS2 are known to be pathogenic (PMID: 11285252, 20177705, 24608809, 26518167).

#	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

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Relating variation to medicine