rs11981364

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_198428.3(BBS9):c.1275+13G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,606,276 control chromosomes in the GnomAD database, including 65,673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5526 hom., cov: 31)

Exomes 𝑓: 0.28 ( 60147 hom. )

Consequence

BBS9
NM_198428.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.538

Publications

8 publications found

Variant links:

Genes affected

BBS9 (HGNC:30000): (Bardet-Biedl syndrome 9) This gene is downregulated by parathyroid hormone in osteoblastic cells, and therefore is thought to be involved in parathyroid hormone action in bones. The exact function of this gene has not yet been determined. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jan 2017]

BBS9 Gene-Disease associations (from GenCC):

Bardet-Biedl syndrome 9
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
ciliopathy
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
Bardet-Biedl syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

BBS9 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 7-33340986-G-T is Benign according to our data. Variant chr7-33340986-G-T is described in ClinVar as [Benign]. Clinvar id is 263114.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BBS9	NM_198428.3 link	c.1275+13G>T		intron_variant	Intron 11 of 22	ENST00000242067.11	NP_940820.1	Q3SYG4-1A0A090N8P4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BBS9	ENST00000242067.11 link	c.1275+13G>T		intron_variant	Intron 11 of 22	1	NM_198428.3	ENSP00000242067.6		Q3SYG4-1

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40100

AN:

151864

Hom.:

5525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.442

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.0749

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.268

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.250

GnomAD2 exomes

AF:

0.240

AC:

60175

AN:

250864

AF XY:

0.243

show subpopulations

Gnomad AFR exome

AF:

0.241

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.251

Gnomad EAS exome

AF:

0.0714

Gnomad FIN exome

AF:

0.273

Gnomad NFE exome

AF:

0.297

Gnomad OTH exome

AF:

0.260

GnomAD4 exome

AF:

0.281

AC:

409159

AN:

1454294

Hom.:

60147

Cov.:

AF XY:

0.279

AC XY:

202325

AN XY:

724008

show subpopulations

African (AFR)

AF:

0.248

AC:

8270

AN:

33342

American (AMR)

AF:

0.150

AC:

6683

AN:

44688

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

6492

AN:

26082

East Asian (EAS)

AF:

0.0514

AC:

2035

AN:

39624

South Asian (SAS)

AF:

0.211

AC:

18205

AN:

86082

European-Finnish (FIN)

AF:

0.276

AC:

14702

AN:

53214

Middle Eastern (MID)

AF:

0.266

AC:

1527

AN:

5750

European-Non Finnish (NFE)

AF:

0.303

AC:

334874

AN:

1105398

Other (OTH)

AF:

0.272

AC:

16371

AN:

60114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

13348

26696

40043

53391

66739

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.264

AC:

40106

AN:

151982

Hom.:

5526

Cov.:

AF XY:

0.258

AC XY:

19182

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.246

AC:

10192

AN:

41474

American (AMR)

AF:

0.208

AC:

3176

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

857

AN:

3468

East Asian (EAS)

AF:

0.0749

AC:

387

AN:

5168

South Asian (SAS)

AF:

0.215

AC:

1034

AN:

4816

European-Finnish (FIN)

AF:

0.268

AC:

2823

AN:

10540

Middle Eastern (MID)

AF:

0.243

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.304

AC:

20641

AN:

67936

Other (OTH)

AF:

0.247

AC:

522

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1485

2970

4456

5941

7426

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.281

Hom.:

1130

Bravo

AF:

0.258

Asia WGS

AF:

0.139

AC:

485

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Bardet-Biedl syndrome 9

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Nov 10, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

7.2

(source)

DANN

Benign

0.79

PhyloP100

-0.54

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs11981364

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over