rs3204173
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017955.4(CDCA4):c.*883A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,554 control chromosomes in the GnomAD database, including 47,575 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 0.79 ( 47464 hom., cov: 33)
Exomes 𝑓: 0.82 ( 111 hom. )
Consequence
CDCA4
NM_017955.4 3_prime_UTR
NM_017955.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.03
Genes affected
CDCA4 (HGNC:14625): (cell division cycle associated 4) This gene encodes a protein that belongs to the E2F family of transcription factors. This protein regulates E2F-dependent transcriptional activation and cell proliferation, mainly through the E2F/retinoblastoma protein pathway. It also functions in the regulation of JUN oncogene expression. This protein shows distinctive nuclear-mitotic apparatus distribution, it is involved in spindle organization from prometaphase, and may also play a role as a midzone factor involved in chromosome segregation or cytokinesis. Two alternatively spliced transcript variants encoding the same protein have been noted for this gene. Two pseudogenes have also been identified on chromosome 1. [provided by RefSeq, May 2014]
CLBA1 (HGNC:20126): (clathrin binding box of aftiphilin containing 1) Predicted to enable clathrin binding activity. Predicted to be involved in intracellular transport. Predicted to be part of AP-1 adaptor complex. Predicted to be active in trans-Golgi network membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDCA4 | NM_017955.4 | c.*883A>G | 3_prime_UTR_variant | 2/2 | ENST00000336219.4 | ||
CDCA4 | NM_145701.4 | c.*357A>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDCA4 | ENST00000336219.4 | c.*883A>G | 3_prime_UTR_variant | 2/2 | 1 | NM_017955.4 | P1 | ||
CDCA4 | ENST00000392590.3 | c.*357A>G | 3_prime_UTR_variant | 3/3 | 1 | P1 | |||
CLBA1 | ENST00000548178.1 | n.304T>C | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.788 AC: 119874AN: 152112Hom.: 47433 Cov.: 33
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GnomAD4 exome AF: 0.821 AC: 266AN: 324Hom.: 111 Cov.: 0 AF XY: 0.785 AC XY: 146AN XY: 186
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GnomAD4 genome ? AF: 0.788 AC: 119960AN: 152230Hom.: 47464 Cov.: 33 AF XY: 0.786 AC XY: 58530AN XY: 74434
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at