rs77298332
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024649.5(BBS1):c.1349G>A(p.Arg450Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00371 in 1,611,024 control chromosomes in the GnomAD database, including 193 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R450W) has been classified as Uncertain significance.
Frequency
Consequence
NM_024649.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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BBS1 | ENST00000318312.12 | c.1349G>A | p.Arg450Gln | missense_variant | Exon 14 of 17 | 1 | NM_024649.5 | ENSP00000317469.7 | ||
ENSG00000256349 | ENST00000419755.3 | c.1460G>A | p.Arg487Gln | missense_variant | Exon 14 of 17 | 2 | ENSP00000398526.3 |
Frequencies
GnomAD3 genomes AF: 0.0197 AC: 2997AN: 151886Hom.: 90 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.00540 AC: 1341AN: 248268 AF XY: 0.00382 show subpopulations
GnomAD4 exome AF: 0.00203 AC: 2968AN: 1459020Hom.: 103 Cov.: 32 AF XY: 0.00172 AC XY: 1247AN XY: 725982 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0198 AC: 3011AN: 152004Hom.: 90 Cov.: 31 AF XY: 0.0189 AC XY: 1405AN XY: 74300 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome 1 Benign:3
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not specified Benign:2
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not provided Benign:1
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Bardet-Biedl syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at