rs141345544
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP3BP6
The NM_033028.5(BBS4):c.864G>A(p.Ala288=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,614,118 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_033028.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BBS4 | NM_033028.5 | c.864G>A | p.Ala288= | splice_region_variant, synonymous_variant | 11/16 | ENST00000268057.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BBS4 | ENST00000268057.9 | c.864G>A | p.Ala288= | splice_region_variant, synonymous_variant | 11/16 | 1 | NM_033028.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000723 AC: 110AN: 152112Hom.: 1 Cov.: 29
GnomAD3 exomes AF: 0.000219 AC: 55AN: 251484Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135916
GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.0000880 AC XY: 64AN XY: 727246
GnomAD4 genome ? AF: 0.000723 AC: 110AN: 152230Hom.: 1 Cov.: 29 AF XY: 0.000672 AC XY: 50AN XY: 74442
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 31, 2020 | Has not been previously published as pathogenic or benign to our knowledge; In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. - |
Bardet-Biedl syndrome 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Dec 20, 2021 | - - |
Bardet-Biedl syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at