12-76346652-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_024685.4(BBS10):c.1333C>A(p.Leu445Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000892 in 1,613,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_024685.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251252Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135814
GnomAD4 exome AF: 0.0000896 AC: 131AN: 1461732Hom.: 0 Cov.: 33 AF XY: 0.000105 AC XY: 76AN XY: 727164
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74320
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome 10 Uncertain:1Benign:1
- -
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
BBS10-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Bardet-Biedl syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at