19-40775859-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006533.4(MIA):c.235C>T(p.Arg79Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,756 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006533.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIA | NM_006533.4 | c.235C>T | p.Arg79Cys | missense_variant | Exon 2 of 4 | ENST00000263369.4 | NP_006524.1 | |
MIA | NM_001202553.2 | c.235C>T | p.Arg79Cys | missense_variant | Exon 3 of 5 | NP_001189482.1 | ||
MIA-RAB4B | NR_037775.1 | n.241C>T | non_coding_transcript_exon_variant | Exon 2 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIA | ENST00000263369.4 | c.235C>T | p.Arg79Cys | missense_variant | Exon 2 of 4 | 1 | NM_006533.4 | ENSP00000263369.2 | ||
MIA-RAB4B | ENST00000600729.2 | n.235C>T | non_coding_transcript_exon_variant | Exon 3 of 11 | 5 | ENSP00000472384.1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151890Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727238
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151890Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74164
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.235C>T (p.R79C) alteration is located in exon 2 (coding exon 2) of the MIA gene. This alteration results from a C to T substitution at nucleotide position 235, causing the arginine (R) at amino acid position 79 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at