3-48180836-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS2_Supporting
The NM_001789.3(CDC25A):āc.434C>Gā(p.Ala145Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000521 in 1,613,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001789.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDC25A | NM_001789.3 | c.434C>G | p.Ala145Gly | missense_variant | 6/15 | ENST00000302506.8 | NP_001780.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC25A | ENST00000302506.8 | c.434C>G | p.Ala145Gly | missense_variant | 6/15 | 1 | NM_001789.3 | ENSP00000303706 | P1 | |
CDC25A | ENST00000351231.7 | c.429+2093C>G | intron_variant | 1 | ENSP00000343166 | |||||
CDC25A | ENST00000443342.5 | c.431C>G | p.Ala144Gly | missense_variant | 6/8 | 3 | ENSP00000416483 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152048Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251402Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135870
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461670Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727130
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152048Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.434C>G (p.A145G) alteration is located in exon 6 (coding exon 6) of the CDC25A gene. This alteration results from a C to G substitution at nucleotide position 434, causing the alanine (A) at amino acid position 145 to be replaced by a glycine (G). 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