rs779604287
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_000900.5(MGP):āc.310T>Cā(p.Ter104Argext*?) variant causes a stop lost change. The variant allele was found at a frequency of 0.000018 in 1,613,842 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 (ā ).
Frequency
Consequence
NM_000900.5 stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MGP | NM_000900.5 | c.310T>C | p.Ter104Argext*? | stop_lost | Exon 4 of 4 | ENST00000539261.6 | NP_000891.2 | |
MGP | NM_001190839.3 | c.385T>C | p.Ter129Argext*? | stop_lost | Exon 5 of 5 | NP_001177768.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152060Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251154Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135710
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727204
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152060Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74272
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change disrupts the translational stop signal of the MGP mRNA. It is expected to extend the length of the MGP protein by 2 additional amino acid residues. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with MGP-related conditions. ClinVar contains an entry for this variant (Variation ID: 2171030). 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