chr16-56514589-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_031885.5(BBS2):c.209G>A(p.Ser70Asn) variant causes a missense change. The variant allele was found at a frequency of 0.993 in 1,614,200 control chromosomes in the GnomAD database, including 796,560 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 1.0 ( 75444 hom., cov: 31)
Exomes 𝑓: 0.99 ( 721116 hom. )
Consequence
BBS2
NM_031885.5 missense
NM_031885.5 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 4.99
Genes affected
BBS2 (HGNC:967): (Bardet-Biedl syndrome 2) This gene is a member of the Bardet-Biedl syndrome (BBS) gene family. Bardet-Biedl syndrome is an autosomal recessive disorder characterized by severe pigmentary retinopathy, obesity, polydactyly, renal malformation and cognitive disability. The proteins encoded by BBS gene family members are structurally diverse and the similar phenotypes exhibited by mutations in BBS gene family members is likely due to their shared roles in cilia formation and function. Many BBS proteins localize to the basal bodies, ciliary axonemes, and pericentriolar regions of cells. BBS proteins may also be involved in intracellular trafficking via microtubule-related transport. The protein encoded by this gene forms a multiprotein BBSome complex with seven other BBS proteins.[provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=6.8563224E-7).
BP6
Variant 16-56514589-C-T is Benign according to our data. Variant chr16-56514589-C-T is described in ClinVar as [Benign]. Clinvar id is 285261.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-56514589-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.995 AC: 151493AN: 152224Hom.: 75385 Cov.: 31
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GnomAD3 exomes AF: 0.994 AC: 249946AN: 251430Hom.: 124238 AF XY: 0.994 AC XY: 135025AN XY: 135902
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GnomAD4 exome AF: 0.993 AC: 1451988AN: 1461858Hom.: 721116 Cov.: 53 AF XY: 0.993 AC XY: 722103AN XY: 727238
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GnomAD4 genome AF: 0.995 AC: 151611AN: 152342Hom.: 75444 Cov.: 31 AF XY: 0.995 AC XY: 74130AN XY: 74504
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TwinsUK
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3682
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3825
ESP6500AA
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4390
ESP6500EA
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8534
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ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Benign:13
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:5
-
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
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Nov 15, 2016
Eurofins Ntd Llc (ga)
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
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Bardet-Biedl syndrome 2 Benign:3
Jul 14, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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May 28, 2019
Mendelics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Nov 16, 2019
Natera, Inc.
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
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Retinal dystrophy Pathogenic:1Benign:1
Oct 01, 2023
Dept Of Ophthalmology, Nagoya University
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: research
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Jan 01, 2013
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing
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not provided Benign:2
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
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Sep 26, 2017
Athena Diagnostics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Retinitis pigmentosa 74 Benign:1
Jul 14, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Bardet-Biedl syndrome Benign:1
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.
MetaRNN
Benign
T;T
MetaSVM
Benign
T
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Vest4
MPC
0.23
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at