chr20-3798450-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021873.4(CDC25B):c.367A>G(p.Met123Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,598,434 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 (★).
Frequency
Consequence
NM_021873.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC25B | NM_021873.4 | c.367A>G | p.Met123Val | missense_variant | 3/16 | ENST00000245960.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC25B | ENST00000245960.10 | c.367A>G | p.Met123Val | missense_variant | 3/16 | 1 | NM_021873.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151530Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000249 AC: 6AN: 240828Hom.: 0 AF XY: 0.0000384 AC XY: 5AN XY: 130342
GnomAD4 exome AF: 0.00000899 AC: 13AN: 1446792Hom.: 0 Cov.: 30 AF XY: 0.00000834 AC XY: 6AN XY: 719370
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151642Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74096
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.367A>G (p.M123V) alteration is located in exon 3 (coding exon 3) of the CDC25B gene. This alteration results from a A to G substitution at nucleotide position 367, causing the methionine (M) at amino acid position 123 to be replaced by a valine (V). 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