10-110900376-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001195305.3(BBIP1):c.263G>A(p.Arg88Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000326 in 1,534,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. 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. R88W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001195305.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000431 AC: 6AN: 139066Hom.: 0 AF XY: 0.0000265 AC XY: 2AN XY: 75416
GnomAD4 exome AF: 0.0000333 AC: 46AN: 1382284Hom.: 0 Cov.: 30 AF XY: 0.0000366 AC XY: 25AN XY: 682156
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74316
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome 18 Uncertain:1
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not provided Uncertain:1
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 88 of the BBIP1 protein (p.Arg88Gln). This variant is present in population databases (rs781040735, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with BBIP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1044270). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Benign". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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. -
BBIP1-related disorder Uncertain:1
The BBIP1 c.263G>A variant is predicted to result in the amino acid substitution p.Arg88Gln. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0084% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at