rs17169807

chr7-33141626-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198428.3(BBS9):c.-11-4616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 152,166 control chromosomes in the GnomAD database, including 548 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.082 (548 hom., cov: 32)
• Consequence: BBS9 NM_198428.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BBS9	NM_198428.3	c.-11-4616T>C		intron_variant		ENST00000242067.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BBS9	ENST00000242067.11	c.-11-4616T>C		intron_variant		1	NM_198428.3	P3

Frequencies

GnomAD3 genomes AF: 0.0824 AC: 12524 AN: 152048 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0590

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0737

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0896

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0824 AC: 12531 AN: 152166 Hom.: 548 Cov.: 32 AF XY: 0.0819 AC XY: 6091 AN XY: 74410

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.0589

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0738

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0819

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.0886

Alfa AF: 0.0811 Hom.: 83

Bravo AF: 0.0821

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.17
Dann	Benign	0.36

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

Other links and lift over

dbSNP: rs17169807; hg19: chr7-33181238;