3-108163675-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018010.4(IFT57):āc.1099A>Cā(p.Met367Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000261 in 1,610,810 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M367T) has been classified as Uncertain significance.
Frequency
Consequence
NM_018010.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT57 | NM_018010.4 | c.1099A>C | p.Met367Leu | missense_variant | 10/11 | ENST00000264538.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT57 | ENST00000264538.4 | c.1099A>C | p.Met367Leu | missense_variant | 10/11 | 1 | NM_018010.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250710Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135494
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1458680Hom.: 0 Cov.: 29 AF XY: 0.0000276 AC XY: 20AN XY: 725746
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 19, 2023 | This sequence change replaces methionine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 367 of the IFT57 protein (p.Met367Leu). This variant is present in population databases (rs750303918, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with IFT57-related conditions. 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