chr7-33467033-T-C

Position:

• chr7-33467033-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_198428.3(BBS9):​c.2116-38430T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.47 (3298 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: BBS9 NM_198428.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BBS9	NM_198428.3	c.2116-38430T>C		intron_variant		ENST00000242067.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BBS9	ENST00000242067.11	c.2116-38430T>C		intron_variant		1	NM_198428.3	P3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 31349 AN: 67284 Hom.: 3294 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.521

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.483

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.466 AC: 31371 AN: 67338 Hom.: 3298 Cov.: 0 AF XY: 0.469 AC XY: 15157 AN XY: 32320

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.483

Alfa AF: 0.124 Hom.: 275

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.62

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: rs4509212; hg19: chr7-33506645;