chr4-122743351-A-C
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_152618.3(BBS12):c.1459A>C(p.Arg487Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R487R) has been classified as Likely benign.
Frequency
Consequence
NM_152618.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- Bardet-Biedl syndrome 12Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, G2P, Ambry Genetics, Myriad Women’s Health
- ciliopathyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- Bardet-Biedl syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BBS12 | NM_152618.3 | c.1459A>C | p.Arg487Arg | synonymous_variant | Exon 2 of 2 | ENST00000314218.8 | NP_689831.2 | |
BBS12 | NM_001178007.2 | c.1459A>C | p.Arg487Arg | synonymous_variant | Exon 3 of 3 | NP_001171478.1 | ||
BBS12 | XM_011531680.3 | c.1459A>C | p.Arg487Arg | synonymous_variant | Exon 2 of 2 | XP_011529982.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BBS12 | ENST00000314218.8 | c.1459A>C | p.Arg487Arg | synonymous_variant | Exon 2 of 2 | 1 | NM_152618.3 | ENSP00000319062.3 | ||
BBS12 | ENST00000542236.5 | c.1459A>C | p.Arg487Arg | synonymous_variant | Exon 3 of 3 | 2 | ENSP00000438273.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251450 AF XY: 0.00000736 show subpopulations
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 727246 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74368 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
ClinVar
Submissions by phenotype
Bardet-Biedl syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at