NM_031885.5(BBS2):c.471G>A (p.Thr157=) AND Bardet-Biedl syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 14, 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:: RCV002532060.3

Allele description [Variation Report for NM_031885.5(BBS2):c.471G>A (p.Thr157=)]

NM_031885.5(BBS2):c.471G>A (p.Thr157=)

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.471G>A (p.Thr157=)

HGVS:

NC_000016.10:g.56511159C>T
NG_009312.2:g.13866G>A
NM_001377456.1:c.471G>A
NM_031885.3:c.[471G>A]
NM_031885.5:c.471G>AMANE SELECT
NP_001364385.1:p.Thr157=
NP_114091.4:p.Thr157=
NC_000016.9:g.56545071C>T
NG_009312.1:g.14125G>A
NM_031885.3:c.471G>A
NM_031885.3:c.[471G>A]
NM_031885.5:c.471G>A
NR_165293.1:n.633G>A
NR_165294.1:n.633G>A
NR_165295.1:n.633G>A
NR_165296.1:n.633G>A
NR_165297.1:n.633G>A

Links:

dbSNP: rs749983428

NCBI 1000 Genomes Browser:

rs749983428

Molecular consequence:

NR_165293.1:n.633G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165294.1:n.633G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165295.1:n.633G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165296.1:n.633G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165297.1:n.633G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001377456.1:c.471G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_031885.5:c.471G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV003443601	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Mar 14, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 17576681, 9536098, 24154662, 29588463, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003443601

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Mar 14, 2023)

germline

clinical testing

PubMed (5)
[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

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 (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003443601.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

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. 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. ClinVar contains an entry for this variant (Variation ID: 551904). This variant has been observed in individuals with Bardet-Biedl syndrome and/or retinitis pigmentosa (PMID: 24154662, 29588463; Invitae). This variant is present in population databases (rs749983428, gnomAD 0.003%). This sequence change affects codon 157 of the BBS2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the BBS2 protein. This variant also falls at the last nucleotide of exon 3, which is part of the consensus splice site for this exon.

#	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: Sep 29, 2024

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