rs4236
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000900.5(MGP):c.304A>T(p.Thr102Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T102A) has been classified as Benign.
Frequency
Consequence
NM_000900.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MGP | NM_000900.5 | c.304A>T | p.Thr102Ser | missense_variant | 4/4 | ENST00000539261.6 | NP_000891.2 | |
MGP | NM_001190839.3 | c.379A>T | p.Thr127Ser | missense_variant | 5/5 | NP_001177768.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MGP | ENST00000539261.6 | c.304A>T | p.Thr102Ser | missense_variant | 4/4 | 1 | NM_000900.5 | ENSP00000445907.1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome Cov.: 49
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at