NM_031885.5(BBS2):c.471G>A (p.Thr157=) AND Bardet-Biedl syndrome 2

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Mar 27, 2024
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:: RCV000667073.7

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 2 (BBS2)
Identifiers:: MONDO: MONDO:0014432; MedGen: C2936863; Orphanet: 110; OMIM: 615981

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000791467	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (May 16, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002073110	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004214015	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 27, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000791467

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(May 16, 2017)

unknown

clinical testing

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

Citation Link,

SCV002073110

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

clinical testing

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

SCV004214015

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 27, 2024)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements.

Wang F, Wang H, Tuan HF, Nguyen DH, Sun V, Keser V, Bowne SJ, Sullivan LS, Luo H, Zhao L, Wang X, Zaneveld JE, Salvo JS, Siddiqui S, Mao L, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Wen C, Flagg K, Ferreyra H, et al.

Hum Genet. 2014 Mar;133(3):331-45. doi: 10.1007/s00439-013-1381-5. Epub 2013 Oct 24.

PubMed [citation]

PMID:: 24154662
PMCID:: PMC3945441

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

Details of each submission

From Counsyl, SCV000791467.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Neuberg Centre For Genomic Medicine, NCGM, SCV002073110.1

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

Description

The synonymous variant p.T157= in BBS2 (NM_031885.5) has been previously reported in an individual with retinis pigmentosa (Wang F et al). The variant has been submitted to ClinVar as Uncertain significance.The p.T157= variant is observed in 1/30,612 (0.0033%) alleles from individuals of South Asian background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The variant affects an invariant splice nucleotide and hence may affect splicing. The p.T157= variant is predicted to disrupt splicing by 3 of 4 splice site algorithms. Since the variant is a synonymous change it is classified as Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004214015.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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