1-100351784-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The ENST00000644676.1(CDC14A):c.28A>G(p.Lys10Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000453 in 1,550,490 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000644676.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC14A | NM_001319211.2 | c.-125-1978A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC14A | ENST00000644676.1 | c.28A>G | p.Lys10Glu | missense_variant | 1/15 | ||||
CDC14A | ENST00000635056.2 | c.-125-1978A>G | intron_variant | 2 | |||||
CDC14A | ENST00000647005.1 | c.-125-1978A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000499 AC: 76AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00129 AC: 192AN: 149232Hom.: 1 AF XY: 0.00114 AC XY: 92AN XY: 80388
GnomAD4 exome AF: 0.000448 AC: 627AN: 1398256Hom.: 3 Cov.: 31 AF XY: 0.000444 AC XY: 306AN XY: 689650
GnomAD4 genome ? AF: 0.000499 AC: 76AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.000471 AC XY: 35AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | CDC14A: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at