Variant chr4-121848809-CTCTT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_176824.3(BBS7):c.934+31_934+34delAAGA variant causes a intron change. The variant allele was found at a frequency of 0.0391 in 1,544,376 control chromosomes in the GnomAD database, including 6,682 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 3373 hom., cov: 30)

Exomes 𝑓: 0.029 ( 3309 hom. )

Consequence

BBS7
NM_176824.3 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.88

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 -16 ACMG points.

BP6

Variant 4-121848809-CTCTT-C is Benign according to our data. Variant chr4-121848809-CTCTT-C is described in ClinVar as [Likely_benign]. Clinvar id is 262923.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-121848809-CTCTT-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BBS7	NM_176824.3 link	c.934+31_934+34delAAGA		intron_variant		ENST00000264499.9	NP_789794.1	Q8IWZ6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BBS7	ENST00000264499.9 link	c.934+31_934+34delAAGA		intron_variant		1	NM_176824.3	ENSP00000264499.4		Q8IWZ6-1
BBS7	ENST00000506636.1 link	c.934+31_934+34delAAGA		intron_variant		1		ENSP00000423626.1		Q8IWZ6-2

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19370

AN:

151826

Hom.:

3362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.395

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0694

Gnomad ASJ

AF:

0.0502

Gnomad EAS

AF:

0.0277

Gnomad SAS

AF:

0.00725

Gnomad FIN

AF:

0.00511

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0204

Gnomad OTH

AF:

0.113

GnomAD3 exomes

AF:

0.0467

AC:

11618

AN:

248794

Hom.:

1477

AF XY:

0.0383

AC XY:

5153

AN XY:

134396

show subpopulations

Gnomad AFR exome

AF:

0.406

Gnomad AMR exome

AF:

0.0328

Gnomad ASJ exome

AF:

0.0547

Gnomad EAS exome

AF:

0.0307

Gnomad SAS exome

AF:

0.00644

Gnomad FIN exome

AF:

0.00397

Gnomad NFE exome

AF:

0.0203

Gnomad OTH exome

AF:

0.0404

GnomAD4 exome

AF:

0.0295

AC:

41012

AN:

1392432

Hom.:

3309

AF XY:

0.0276

AC XY:

19258

AN XY:

696846

show subpopulations

Gnomad4 AFR exome

AF:

0.416

Gnomad4 AMR exome

AF:

0.0370

Gnomad4 ASJ exome

AF:

0.0554

Gnomad4 EAS exome

AF:

0.0244

Gnomad4 SAS exome

AF:

0.00696

Gnomad4 FIN exome

AF:

0.00521

Gnomad4 NFE exome

AF:

0.0186

Gnomad4 OTH exome

AF:

0.0481

GnomAD4 genome

AF:

0.128

AC:

19422

AN:

151944

Hom.:

3373

Cov.:

AF XY:

0.123

AC XY:

9132

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.395

Gnomad4 AMR

AF:

0.0691

Gnomad4 ASJ

AF:

0.0502

Gnomad4 EAS

AF:

0.0280

Gnomad4 SAS

AF:

0.00684

Gnomad4 FIN

AF:

0.00511

Gnomad4 NFE

AF:

0.0204

Gnomad4 OTH

AF:

0.112

Alfa

AF:

0.0704

Hom.:

256

Bravo

AF:

0.148

Asia WGS

AF:

0.0400

AC:

139

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

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

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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