X-55221788-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001013435.3(PAGE5):āc.103A>Gā(p.Lys35Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,208,128 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001013435.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAGE5 | NM_001013435.3 | c.103A>G | p.Lys35Glu | missense_variant | 3/5 | ENST00000374955.8 | |
PAGE5 | NM_130467.5 | c.163A>G | p.Lys55Glu | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAGE5 | ENST00000374955.8 | c.103A>G | p.Lys35Glu | missense_variant | 3/5 | 1 | NM_001013435.3 | P2 | |
PAGE5 | ENST00000289619.9 | c.163A>G | p.Lys55Glu | missense_variant | 3/5 | 1 | A2 | ||
PAGE5 | ENST00000374952.1 | c.103A>G | p.Lys35Glu | missense_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111434Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33614
GnomAD3 exomes AF: 0.00000559 AC: 1AN: 178953Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 63779
GnomAD4 exome AF: 0.00000365 AC: 4AN: 1096694Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1AN XY: 362282
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111434Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33614
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 27, 2023 | The c.163A>G (p.K55E) alteration is located in exon 3 (coding exon 3) of the PAGE5 gene. This alteration results from a A to G substitution at nucleotide position 163, causing the lysine (K) at amino acid position 55 to be replaced by a glutamic acid (E). 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