rs17169881

Positions:

• chr7-33152890-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.0240

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]

ACMG classification

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/exons	MANE	UniProt
BBS9	NM_198428.3	c.263+39A>G		intron_variant		ENST00000242067.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BBS9	ENST00000242067.11	c.263+39A>G		intron_variant		1	NM_198428.3	P3

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24598 AN: 152012 Hom.: 2137 Cov.: 31

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

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.: 29 AF XY: 0.190 AC XY: 137210 AN XY: 720838

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.: 31 AF XY: 0.164 AC XY: 12170 AN XY: 74378

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

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

-

- -

Bardet-Biedl syndrome 9 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
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

Other links and lift over

dbSNP: rs17169881; hg19: chr7-33192502; COSMIC: COSV54181849; COSMIC: COSV54181849;