rs753478409
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020800.3(IFT80):c.938C>T(p.Thr313Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,612,556 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T313A) has been classified as Likely benign.
Frequency
Consequence
NM_020800.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT80 | NM_020800.3 | c.938C>T | p.Thr313Met | missense_variant | 9/20 | ENST00000326448.12 | |
TRIM59-IFT80 | NR_148401.1 | n.1646C>T | non_coding_transcript_exon_variant | 7/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT80 | ENST00000326448.12 | c.938C>T | p.Thr313Met | missense_variant | 9/20 | 1 | NM_020800.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151838Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250988Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135636
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460718Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726666
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151838Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74152
ClinVar
Submissions by phenotype
Jeune thoracic dystrophy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2019 | 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. This variant has not been reported in the literature in individuals with IFT80-related conditions. ClinVar contains an entry for this variant (Variation ID: 216710). This variant is present in population databases (rs753478409, ExAC 0.01%). This sequence change replaces threonine with methionine at codon 313 of the IFT80 protein (p.Thr313Met). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and methionine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at