chr2-169479578-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152384.3(BBS5):c.25G>C(p.Glu9Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,842 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E9K) has been classified as Uncertain significance.
Frequency
Consequence
NM_152384.3 missense
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 |
---|---|---|---|---|---|---|---|
BBS5 | NM_152384.3 | c.25G>C | p.Glu9Gln | missense_variant | 1/12 | ENST00000295240.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BBS5 | ENST00000295240.8 | c.25G>C | p.Glu9Gln | missense_variant | 1/12 | 1 | NM_152384.3 | P1 | |
BBS5 | ENST00000392663.6 | c.25G>C | p.Glu9Gln | missense_variant | 1/11 | 1 | |||
BBS5 | ENST00000469980.1 | n.99G>C | non_coding_transcript_exon_variant | 1/2 | 4 | ||||
BBS5 | ENST00000443151.1 | c.25G>C | p.Glu9Gln | missense_variant, NMD_transcript_variant | 1/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249794Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135152
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461842Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727228
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 09, 2022 | This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 9 of the BBS5 protein (p.Glu9Gln). This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with BBS5-related conditions. ClinVar contains an entry for this variant (Variation ID: 958031). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at