chr4-22736185-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000508166.5(GBA3):c.263C>T(p.Thr88Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,386 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T88A) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000508166.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GBA3 | NR_102355.2 | n.342C>T | non_coding_transcript_exon_variant | 2/5 | |||
LOC105374521 | XR_007058431.1 | n.860-2493G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GBA3 | ENST00000508166.5 | c.263C>T | p.Thr88Met | missense_variant | 2/5 | 1 | P5 | ||
GBA3 | ENST00000503442.1 | c.263C>T | p.Thr88Met | missense_variant | 2/3 | 1 | A2 | ||
GBA3 | ENST00000511446.2 | c.-251C>T | 5_prime_UTR_variant | 2/5 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248024Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134616
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461302Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726946
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.263C>T (p.T88M) alteration is located in exon 2 (coding exon 2) of the GBA3 gene. This alteration results from a C to T substitution at nucleotide position 263, causing the threonine (T) at amino acid position 88 to be replaced by a methionine (M). 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