Variant rs56159666 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_176824.3(BBS7):c.166-45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 1,599,604 control chromosomes in the GnomAD database, including 76,088 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6192 hom., cov: 32)

Exomes 𝑓: 0.31 ( 69896 hom. )

Consequence

BBS7
NM_176824.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.239

Variant links:

Genes affected

BBS7 (HGNC:18758): (Bardet-Biedl syndrome 7) This gene encodes one of eight proteins that form the BBSome complex containing BBS1, BBS2, BBS4, BBS5, BBS7, BBS8, BBS9 and BBIP10. The BBSome complex is believed to recruit Rab8(GTP) to the primary cilium and promote ciliogenesis. The BBSome complex assembly is mediated by a complex composed of three chaperonin-like BBS proteins (BBS6, BBS10, and BBS12) and CCT/TRiC family chaperonins. Mutations in this gene are implicated in Bardet-Biedl syndrome, a genetic disorder whose symptoms include obesity, retinal degeneration, polydactyly and nephropathy; however, mutations in this gene and the BBS8 gene are thought to play a minor role and mutations in chaperonin-like BBS genes are found to be a major contributor to disease development in a multiethnic Bardet-Biedl syndrome patient population. Two transcript variants encoding distinct isoforms have been identified for this gene.[provided by RefSeq, Oct 2014]

BBS7 links:

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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 (BayesDel_noAF=-0.83).

BP6

Variant 4-121861724-G-A is Benign according to our data. Variant chr4-121861724-G-A is described in ClinVar as [Benign]. Clinvar id is 262919.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-121861724-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BBS7	NM_176824.3 link	c.166-45C>T		intron_variant		ENST00000264499.9	NP_789794.1	Q8IWZ6-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
BBS7	ENST00000264499.9 link	c.166-45C>T	intron_variant	1	NM_176824.3	ENSP00000264499.4	Q8IWZ6-1
BBS7	ENST00000506636.1 link	c.166-45C>T	intron_variant	1		ENSP00000423626.1	Q8IWZ6-2
BBS7	ENST00000502444.1 link	n.340-45C>T	intron_variant	2
BBS7	ENST00000505692.1 link	n.-45C>T	upstream_gene_variant	2

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41073

AN:

151770

Hom.:

6189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.299

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.275

GnomAD3 exomes

AF:

0.305

AC:

73192

AN:

240332

Hom.:

11465

AF XY:

0.308

AC XY:

40272

AN XY:

130758

show subpopulations

Gnomad AFR exome

AF:

0.143

Gnomad AMR exome

AF:

0.310

Gnomad ASJ exome

AF:

0.314

Gnomad EAS exome

AF:

0.197

Gnomad SAS exome

AF:

0.323

Gnomad FIN exome

AF:

0.373

Gnomad NFE exome

AF:

0.324

Gnomad OTH exome

AF:

0.294

GnomAD4 exome

AF:

0.308

AC:

445409

AN:

1447712

Hom.:

69896

Cov.:

AF XY:

0.310

AC XY:

223272

AN XY:

720476

show subpopulations

Gnomad4 AFR exome

AF:

0.137

Gnomad4 AMR exome

AF:

0.311

Gnomad4 ASJ exome

AF:

0.319

Gnomad4 EAS exome

AF:

0.185

Gnomad4 SAS exome

AF:

0.319

Gnomad4 FIN exome

AF:

0.365

Gnomad4 NFE exome

AF:

0.314

Gnomad4 OTH exome

AF:

0.290

GnomAD4 genome

AF:

0.270

AC:

41086

AN:

151892

Hom.:

6192

Cov.:

AF XY:

0.274

AC XY:

20354

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.147

Gnomad4 AMR

AF:

0.304

Gnomad4 ASJ

AF:

0.315

Gnomad4 EAS

AF:

0.198

Gnomad4 SAS

AF:

0.301

Gnomad4 FIN

AF:

0.381

Gnomad4 NFE

AF:

0.322

Gnomad4 OTH

AF:

0.276

Alfa

AF:

0.313

Hom.:

1422

Bravo

AF:

0.256

Asia WGS

AF:

0.228

AC:

792

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.3

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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