chrX-49694736-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003785.4(PAGE1):c.35G>A(p.Arg12Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,197,836 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 63 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003785.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000624 AC: 7AN: 112248Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34414
GnomAD3 exomes AF: 0.0000897 AC: 16AN: 178349Hom.: 0 AF XY: 0.0000635 AC XY: 4AN XY: 62963
GnomAD4 exome AF: 0.000205 AC: 223AN: 1085588Hom.: 0 Cov.: 24 AF XY: 0.000176 AC XY: 62AN XY: 351838
GnomAD4 genome AF: 0.0000624 AC: 7AN: 112248Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34414
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.35G>A (p.R12K) alteration is located in exon 2 (coding exon 1) of the PAGE1 gene. This alteration results from a G to A substitution at nucleotide position 35, causing the arginine (R) at amino acid position 12 to be replaced by a lysine (K). 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