13-20574471-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_006531.5(IFT88):āc.86T>Cā(p.Ile29Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000153 in 1,576,908 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_006531.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFT88 | NM_006531.5 | c.86T>C | p.Ile29Thr | 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.86T>C | p.Ile29Thr | missense_variant | Exon 2 of 26 | 1 | NM_006531.5 | ENSP00000261632.5 | ||
IFT88 | ENST00000319980.10 | c.113T>C | p.Ile38Thr | missense_variant | Exon 4 of 28 | 1 | ENSP00000323580.6 | |||
IFT88 | ENST00000389373.3 | c.86T>C | p.Ile29Thr | missense_variant | Exon 3 of 4 | 4 | ENSP00000374024.3 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000441 AC: 109AN: 247314Hom.: 1 AF XY: 0.000389 AC XY: 52AN XY: 133664
GnomAD4 exome AF: 0.000145 AC: 207AN: 1424588Hom.: 1 Cov.: 23 AF XY: 0.000132 AC XY: 94AN XY: 710636
GnomAD4 genome AF: 0.000230 AC: 35AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:2
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IFT88-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at