chr5-55226608-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_001190787.3(MCIDAS):c.277G>A(p.Ala93Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000029 in 1,380,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict 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. A93P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001190787.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCIDAS | NM_001190787.3 | c.277G>A | p.Ala93Thr | missense_variant | 3/7 | ENST00000513312.3 | |
LOC124900978 | XR_007058773.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCIDAS | ENST00000513312.3 | c.277G>A | p.Ala93Thr | missense_variant | 3/7 | 1 | NM_001190787.3 | P1 | |
MCIDAS | ENST00000515336.1 | n.214G>A | non_coding_transcript_exon_variant | 3/6 | 5 | ||||
MCIDAS | ENST00000513468.5 | c.277G>A | p.Ala93Thr | missense_variant, NMD_transcript_variant | 3/7 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000290 AC: 4AN: 1380060Hom.: 0 Cov.: 31 AF XY: 0.00000147 AC XY: 1AN XY: 680994
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2023 | 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MCIDAS protein function. This variant has not been reported in the literature in individuals affected with MCIDAS-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 93 of the MCIDAS protein (p.Ala93Thr). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at