13-20574403-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006531.5(IFT88):āc.18C>Gā(p.His6Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,458,174 control chromosomes in the GnomAD database, including 1 homozygotes. 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 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFT88 | NM_006531.5 | c.18C>G | p.His6Gln | missense_variant | 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.18C>G | p.His6Gln | missense_variant | Exon 2 of 26 | 1 | NM_006531.5 | ENSP00000261632.5 | ||
IFT88 | ENST00000319980.10 | c.45C>G | p.His15Gln | missense_variant | Exon 4 of 28 | 1 | ENSP00000323580.6 | |||
IFT88 | ENST00000389373.3 | c.18C>G | p.His6Gln | missense_variant | Exon 3 of 4 | 4 | ENSP00000374024.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250182Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135268
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1458174Hom.: 1 Cov.: 28 AF XY: 0.0000248 AC XY: 18AN XY: 725506
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces histidine, which is basic and polar, with glutamine, which is neutral and polar, at codon 15 of the IFT88 protein (p.His15Gln). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with IFT88-related conditions. ClinVar contains an entry for this variant (Variation ID: 1965773). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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