rs747388658
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Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_198428.3(BBS9):c.309_310delTT(p.Val105fs) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000558 in 1,433,532 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000056 ( 0 hom. )
Consequence
BBS9
NM_198428.3 frameshift
NM_198428.3 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.70
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BBS9 | NM_198428.3 | c.309_310delTT | p.Val105fs | frameshift_variant | 4/23 | ENST00000242067.11 | NP_940820.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248184Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134228
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GnomAD4 exome AF: 0.00000558 AC: 8AN: 1433532Hom.: 0 AF XY: 0.00000280 AC XY: 2AN XY: 714440
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GnomAD4 genome Cov.: 30
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ClinVar
Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at