chr19-34368601-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 8P and 4B. PS1_ModeratePP3_StrongPP5_ModerateBS2
The NM_000175.5(GPI):c.301G>A(p.Val101Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000867 in 1,614,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_000175.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPI | NM_000175.5 | c.301G>A | p.Val101Met | missense_variant | 4/18 | ENST00000356487.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPI | ENST00000356487.11 | c.301G>A | p.Val101Met | missense_variant | 4/18 | 1 | NM_000175.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251424Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135916
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461854Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 727234
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
Hemolytic anemia due to glucophosphate isomerase deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | provider interpretation | Department of Endocrinology, The Children’s Hospital of Zhejiang University School of Medicine | Feb 01, 2022 | Note: This variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Therefore, any internal case data may overlap with the internal case data of other submitters. The interpretation and rationale are that of the Department of Endocrinology, The Children’s Hospital of Zhejiang University School of Medicine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at