rs775081992
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_001348038.3(BBS9):c.-55C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.00000753 in 1,461,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_001348038.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BBS9 | NM_198428.3 | c.223C>T | p.Arg75* | stop_gained | Exon 3 of 23 | ENST00000242067.11 | NP_940820.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251294Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135822
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461610Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727122
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome 9 Pathogenic:3
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Bardet-Biedl syndrome Pathogenic:2
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This sequence change creates a premature translational stop signal (p.Arg75*) in the BBS9 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BBS9 are known to be pathogenic (PMID: 16380913, 20177705). This variant is present in population databases (rs775081992, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with clinical features of Bardet-Biedl syndrome (PMID: 31488071). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 266106). For these reasons, this variant has been classified as Pathogenic. -
BBS9-related disorder Pathogenic:1
The BBS9 c.223C>T variant is predicted to result in premature protein termination (p.Arg75*). This variant has been reported in the compound heterozygous state in two unrelated patients with Bardet-Biedl syndrome (Shaheen et al. 2016. PubMed ID: 27894351, Table S3; Niazi et al. 2019. PubMed ID: 31488071). We have detected this variant at PreventionGenetics in the compound heterozygous and homozygous states in two patients with BBS. This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-33192423-C-T). Nonsense variants in BBS9 are expected to be pathogenic. This variant is interpreted as pathogenic. -
Retinal vascular dystrophy Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at