rs58665245
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The ENST00000326448.12(IFT80):c.2224-13_2224-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000594 in 1,514,150 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000044 ( 0 hom. )
Consequence
IFT80
ENST00000326448.12 splice_polypyrimidine_tract, intron
ENST00000326448.12 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.62
Genes affected
IFT80 (HGNC:29262): (intraflagellar transport 80) The protein encoded by this gene is part of the intraflagellar transport complex B and is necessary for the function of motile and sensory cilia. Defects in this gene are a cause of asphyxiating thoracic dystrophy 2 (ATD2). Three transcript variants encoding two different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 3-160258644-GAAAA-G is Benign according to our data. Variant chr3-160258644-GAAAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 1590050.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFT80 | NM_020800.3 | c.2224-13_2224-10del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000326448.12 | NP_065851.1 | |||
TRIM59-IFT80 | NR_148401.1 | n.2932-13_2932-10del | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFT80 | ENST00000326448.12 | c.2224-13_2224-10del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020800.3 | ENSP00000312778 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000203 AC: 3AN: 147972Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.00000534 AC: 1AN: 187270Hom.: 0 AF XY: 0.00000986 AC XY: 1AN XY: 101404
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GnomAD4 exome AF: 0.00000439 AC: 6AN: 1366178Hom.: 0 AF XY: 0.00000441 AC XY: 3AN XY: 679782
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GnomAD4 genome AF: 0.0000203 AC: 3AN: 147972Hom.: 0 Cov.: 0 AF XY: 0.0000278 AC XY: 2AN XY: 71944
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Jeune thoracic dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 17, 2022 | - - |
Computational scores
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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