X-49691373-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003785.4(PAGE1):c.168G>A(p.Gly56Gly) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00539 in 1,189,221 control chromosomes in the GnomAD database, including 16 homozygotes. There are 2,070 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003785.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAGE1 | NM_003785.4 | c.168G>A | p.Gly56Gly | splice_region_variant, synonymous_variant | Exon 4 of 6 | ENST00000376150.4 | NP_003776.2 | |
PAGE1 | XM_011543998.3 | c.168G>A | p.Gly56Gly | splice_region_variant, synonymous_variant | Exon 4 of 6 | XP_011542300.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00371 AC: 413AN: 111449Hom.: 1 Cov.: 23 AF XY: 0.00339 AC XY: 114AN XY: 33669
GnomAD3 exomes AF: 0.00348 AC: 589AN: 169157Hom.: 0 AF XY: 0.00373 AC XY: 212AN XY: 56857
GnomAD4 exome AF: 0.00557 AC: 6000AN: 1077721Hom.: 15 Cov.: 26 AF XY: 0.00565 AC XY: 1956AN XY: 346501
GnomAD4 genome AF: 0.00370 AC: 413AN: 111500Hom.: 1 Cov.: 23 AF XY: 0.00338 AC XY: 114AN XY: 33730
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at