dbSNP rs17169881: BBS9:c.263+39A>G (chr7-33152890-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_198428.3(BBS9):c.263+39A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,599,346 control chromosomes in the GnomAD database, including 28,741 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2142 hom., cov: 31)

Exomes 𝑓: 0.19 ( 26599 hom. )

Consequence

BBS9
NM_198428.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0240

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 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=-0.84).

BP6

Variant 7-33152890-A-G is Benign according to our data. Variant chr7-33152890-A-G is described in ClinVar as [Benign]. Clinvar id is 263126.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BBS9	NM_198428.3 link	c.263+39A>G		intron_variant	Intron 3 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.263+39A>G		intron_variant	Intron 3 of 22	1	NM_198428.3	ENSP00000242067.6		Q3SYG4-1

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24598

AN:

152012

Hom.:

2137

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0976

Gnomad AMI

AF:

0.0844

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.208

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.178

GnomAD3 exomes

AF:

0.190

AC:

47691

AN:

250530

Hom.:

4822

AF XY:

0.194

AC XY:

26230

AN XY:

135428

show subpopulations

Gnomad AFR exome

AF:

0.0965

Gnomad AMR exome

AF:

0.221

Gnomad ASJ exome

AF:

0.194

Gnomad EAS exome

AF:

0.167

Gnomad SAS exome

AF:

0.232

Gnomad FIN exome

AF:

0.205

Gnomad NFE exome

AF:

0.184

Gnomad OTH exome

AF:

0.186

GnomAD4 exome

AF:

0.188

AC:

272463

AN:

1447216

Hom.:

26599

Cov.:

AF XY:

0.190

AC XY:

137210

AN XY:

720838

show subpopulations

Gnomad4 AFR exome

AF:

0.0943

Gnomad4 AMR exome

AF:

0.210

Gnomad4 ASJ exome

AF:

0.186

Gnomad4 EAS exome

AF:

0.132

Gnomad4 SAS exome

AF:

0.234

Gnomad4 FIN exome

AF:

0.205

Gnomad4 NFE exome

AF:

0.188

Gnomad4 OTH exome

AF:

0.185

GnomAD4 genome

AF:

0.162

AC:

24633

AN:

152130

Hom.:

2142

Cov.:

AF XY:

0.164

AC XY:

12170

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.0982

Gnomad4 AMR

AF:

0.178

Gnomad4 ASJ

AF:

0.182

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.208

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.180

Alfa

AF:

0.179

Hom.:

573

Bravo

AF:

0.156

Asia WGS

AF:

0.201

AC:

698

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Bardet-Biedl syndrome 9

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Nov 10, 2018

GeneDx

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

-0.84

CADD

Benign

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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