5-138289452-C-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001790.5(CDC25C):c.927+49G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 1,335,852 control chromosomes in the GnomAD database, including 206 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.011 ( 13 hom., cov: 32)
Exomes 𝑓: 0.014 ( 193 hom. )
Consequence
CDC25C
NM_001790.5 intron
NM_001790.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0660
Genes affected
CDC25C (HGNC:1727): (cell division cycle 25C) This gene encodes a conserved protein that plays a key role in the regulation of cell division. The encoded protein directs dephosphorylation of cyclin B-bound CDC2 and triggers entry into mitosis. It also suppresses p53-induced growth arrest. Multiple alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0105 (1599/152212) while in subpopulation NFE AF= 0.0163 (1107/68026). AF 95% confidence interval is 0.0155. There are 13 homozygotes in gnomad4. There are 705 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 13 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDC25C | NM_001790.5 | c.927+49G>C | intron_variant | ENST00000323760.11 | NP_001781.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC25C | ENST00000323760.11 | c.927+49G>C | intron_variant | 1 | NM_001790.5 | ENSP00000321656.6 |
Frequencies
GnomAD3 genomes AF: 0.0105 AC: 1600AN: 152094Hom.: 13 Cov.: 32
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GnomAD3 exomes AF: 0.0101 AC: 2539AN: 250698Hom.: 24 AF XY: 0.0105 AC XY: 1425AN XY: 135498
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GnomAD4 exome AF: 0.0143 AC: 16908AN: 1183640Hom.: 193 Cov.: 17 AF XY: 0.0140 AC XY: 8431AN XY: 602026
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GnomAD4 genome AF: 0.0105 AC: 1599AN: 152212Hom.: 13 Cov.: 32 AF XY: 0.00947 AC XY: 705AN XY: 74422
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at