chr19-34364916-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001289789.1(GPI):c.7G>A(p.Ala3Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000237 in 1,469,542 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001289789.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPI | NM_001289789.1 | c.7G>A | p.Ala3Thr | missense_variant | 1/19 | ||
GPI | NM_001184722.1 | c.7G>A | p.Ala3Thr | missense_variant | 1/18 | ||
GPI | XM_011526754.4 | c.7G>A | p.Ala3Thr | missense_variant | 2/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPI | ENST00000415930.8 | c.7G>A | p.Ala3Thr | missense_variant | 1/19 | 2 | |||
GPI | ENST00000588991.7 | c.7G>A | p.Ala3Thr | missense_variant | 1/18 | 2 | |||
GPI | ENST00000592277.5 | c.7G>A | p.Ala3Thr | missense_variant | 2/6 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00125 AC: 190AN: 152226Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000171 AC: 21AN: 122978Hom.: 0 AF XY: 0.000119 AC XY: 8AN XY: 67252
GnomAD4 exome AF: 0.000120 AC: 158AN: 1317198Hom.: 0 Cov.: 21 AF XY: 0.0000907 AC XY: 59AN XY: 650686
GnomAD4 genome ? AF: 0.00125 AC: 190AN: 152344Hom.: 1 Cov.: 32 AF XY: 0.00107 AC XY: 80AN XY: 74488
ClinVar
Submissions by phenotype
Hemolytic anemia due to glucophosphate isomerase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jan 25, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at