Variant rs79900021 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_031885.5(BBS2):c.718-34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0467 in 1,609,490 control chromosomes in the GnomAD database, including 2,567 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 209 hom., cov: 32)

Exomes 𝑓: 0.047 ( 2358 hom. )

Consequence

BBS2
NM_031885.5 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.656

Variant links:

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]

BBS2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 16-56506070-C-T is Benign according to our data. Variant chr16-56506070-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 261983.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BBS2	NM_031885.5 linkuse as main transcript	c.718-34G>A		intron_variant		ENST00000245157.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BBS2	ENST00000245157.11 linkuse as main transcript	c.718-34G>A		intron_variant		1	NM_031885.5	P1

Frequencies

GnomAD3 genomes

AF:

0.0422

AC:

6422

AN:

152160

Hom.:

210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0236

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0328

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.156

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.0510

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0410

Gnomad OTH

AF:

0.0392

GnomAD3 exomes

AF:

0.0600

AC:

15027

AN:

250482

Hom.:

729

AF XY:

0.0635

AC XY:

8607

AN XY:

135458

show subpopulations

Gnomad AFR exome

AF:

0.0239

Gnomad AMR exome

AF:

0.0450

Gnomad ASJ exome

AF:

0.0176

Gnomad EAS exome

AF:

0.170

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.0454

Gnomad NFE exome

AF:

0.0402

Gnomad OTH exome

AF:

0.0531

GnomAD4 exome

AF:

0.0472

AC:

68788

AN:

1457214

Hom.:

2358

Cov.:

AF XY:

0.0495

AC XY:

35873

AN XY:

725304

show subpopulations

Gnomad4 AFR exome

AF:

0.0239

Gnomad4 AMR exome

AF:

0.0419

Gnomad4 ASJ exome

AF:

0.0180

Gnomad4 EAS exome

AF:

0.122

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.0448

Gnomad4 NFE exome

AF:

0.0399

Gnomad4 OTH exome

AF:

0.0523

GnomAD4 genome

AF:

0.0422

AC:

6424

AN:

152276

Hom.:

209

Cov.:

AF XY:

0.0448

AC XY:

3336

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0236

Gnomad4 AMR

AF:

0.0329

Gnomad4 ASJ

AF:

0.0153

Gnomad4 EAS

AF:

0.155

Gnomad4 SAS

AF:

0.135

Gnomad4 FIN

AF:

0.0510

Gnomad4 NFE

AF:

0.0410

Gnomad4 OTH

AF:

0.0416

Alfa

AF:

0.0399

Hom.:

Bravo

AF:

0.0392

Asia WGS

AF:

0.156

AC:

542

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Retinitis pigmentosa 74

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Bardet-Biedl syndrome 2

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

Cadd

Benign

9.2

Dann

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over