4-22693071-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The ENST00000508166.5(GBA3):āc.56A>Gā(p.Glu19Gly) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000192 in 1,455,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000508166.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GBA3 | NR_102355.2 | n.135A>G | splice_region_variant, non_coding_transcript_exon_variant | 1/5 | |||
GBA3 | NR_102356.2 | n.135A>G | splice_region_variant, non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GBA3 | ENST00000508166.5 | c.56A>G | p.Glu19Gly | missense_variant, splice_region_variant | 1/5 | 1 | P5 | ||
GBA3 | ENST00000503442.1 | c.56A>G | p.Glu19Gly | missense_variant, splice_region_variant | 1/3 | 1 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000838 AC: 2AN: 238748Hom.: 0 AF XY: 0.00000775 AC XY: 1AN XY: 129008
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1455934Hom.: 0 Cov.: 30 AF XY: 0.0000221 AC XY: 16AN XY: 723544
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.56A>G (p.E19G) alteration is located in exon 1 (coding exon 1) of the GBA3 gene. This alteration results from a A to G substitution at nucleotide position 56, causing the glutamic acid (E) at amino acid position 19 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at