13-20574386-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_SupportingPM2
The NM_006531.5(IFT88):āc.1A>Gā(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.0000598 in 1,606,362 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 Uncertain significance (ā ).
Frequency
Consequence
NM_006531.5 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFT88 | NM_006531.5 | c.1A>G | p.Met1? | start_lost | Exon 2 of 26 | ENST00000351808.10 | NP_006522.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFT88 | ENST00000351808.10 | c.1A>G | p.Met1? | start_lost | Exon 2 of 26 | 1 | NM_006531.5 | ENSP00000261632.5 | ||
IFT88 | ENST00000319980.10 | c.28A>G | p.Met10Val | missense_variant | Exon 4 of 28 | 1 | ENSP00000323580.6 | |||
IFT88 | ENST00000389373.3 | c.1A>G | p.Met1? | start_lost | Exon 3 of 4 | 4 | ENSP00000374024.3 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000152 AC: 38AN: 249890Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135130
GnomAD4 exome AF: 0.0000557 AC: 81AN: 1454012Hom.: 0 Cov.: 28 AF XY: 0.0000608 AC XY: 44AN XY: 723634
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74512
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 10 of the IFT88 protein (p.Met10Val). This variant is present in population databases (rs191277814, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with IFT88-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at