rs748809549
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM5
The NM_021971.4(GMPPB):c.878G>T(p.Arg293Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,272 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R293W) has been classified as Uncertain significance.
Frequency
Consequence
NM_021971.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GMPPB | NM_021971.4 | c.878G>T | p.Arg293Leu | missense_variant | 8/9 | ENST00000308388.7 | |
GMPPB | NM_013334.4 | c.878G>T | p.Arg293Leu | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GMPPB | ENST00000308388.7 | c.878G>T | p.Arg293Leu | missense_variant | 8/9 | 1 | NM_021971.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250196Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135450
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461272Hom.: 0 Cov.: 43 AF XY: 0.00000275 AC XY: 2AN XY: 726954
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at