chr15-69268747-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015554.3(GLCE):āc.1357A>Gā(p.Thr453Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T453I) has been classified as Uncertain significance.
Frequency
Consequence
NM_015554.3 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 |
---|---|---|---|---|---|---|---|
GLCE | NM_015554.3 | c.1357A>G | p.Thr453Ala | missense_variant | 5/5 | ENST00000261858.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLCE | ENST00000261858.7 | c.1357A>G | p.Thr453Ala | missense_variant | 5/5 | 1 | NM_015554.3 | P1 | |
GLCE | ENST00000559420.2 | c.1165A>G | p.Thr389Ala | missense_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251388Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135876
GnomAD4 exome AF: 0.0000965 AC: 141AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.0000935 AC XY: 68AN XY: 727240
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.1357A>G (p.T453A) alteration is located in exon 5 (coding exon 3) of the GLCE gene. This alteration results from a A to G substitution at nucleotide position 1357, causing the threonine (T) at amino acid position 453 to be replaced by an alanine (A). 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