4-122741906-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152618.3(BBS12):c.14G>T(p.Cys5Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,782 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 Uncertain significance (no stars).
Frequency
Consequence
NM_152618.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BBS12 | NM_152618.3 | c.14G>T | p.Cys5Phe | missense_variant | 2/2 | ENST00000314218.8 | NP_689831.2 | |
BBS12 | NM_001178007.2 | c.14G>T | p.Cys5Phe | missense_variant | 3/3 | NP_001171478.1 | ||
BBS12 | XM_011531680.3 | c.14G>T | p.Cys5Phe | missense_variant | 2/2 | XP_011529982.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BBS12 | ENST00000314218.8 | c.14G>T | p.Cys5Phe | missense_variant | 2/2 | 1 | NM_152618.3 | ENSP00000319062 | P1 | |
BBS12 | ENST00000542236.5 | c.14G>T | p.Cys5Phe | missense_variant | 3/3 | 2 | ENSP00000438273 | P1 | ||
BBS12 | ENST00000433287.1 | c.14G>T | p.Cys5Phe | missense_variant | 3/3 | 2 | ENSP00000398912 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727188
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
BBS12-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 07, 2024 | The BBS12 c.14G>T variant is predicted to result in the amino acid substitution p.Cys5Phe. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. 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
Publications
No publications associated with this variant yet.