rs1402769479
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006531.5(IFT88):c.-7+765delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000178 in 561,326 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000018 ( 0 hom. )
Consequence
IFT88
NM_006531.5 intron
NM_006531.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.378
Genes affected
IFT88 (HGNC:20606): (intraflagellar transport 88) This gene encodes a member of the tetratrico peptide repeat (TPR) family. The encoded protein is involved in cilium biogenesis. Mutations of a similar gene in mouse can cause polycystic kidney disease. Several transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFT88 | NM_006531.5 | c.-7+765delA | intron_variant | Intron 1 of 25 | ENST00000351808.10 | NP_006522.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFT88 | ENST00000351808.10 | c.-7+758delA | intron_variant | Intron 1 of 25 | 1 | NM_006531.5 | ENSP00000261632.5 | |||
IFT88 | ENST00000319980.10 | c.21+17delA | intron_variant | Intron 3 of 27 | 1 | ENSP00000323580.6 | ||||
IFT88 | ENST00000389373.3 | c.-7+17delA | intron_variant | Intron 2 of 3 | 4 | ENSP00000374024.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000178 AC: 1AN: 561326Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 303264
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
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ClinVar
Not reported inComputational scores
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at