rs9797
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018246.3(CCDC25):c.*1884C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,036 control chromosomes in the GnomAD database, including 14,324 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 0.42 ( 14321 hom., cov: 32)
Exomes 𝑓: 0.50 ( 3 hom. )
Consequence
CCDC25
NM_018246.3 3_prime_UTR
NM_018246.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.642
Genes affected
CCDC25 (HGNC:25591): (coiled-coil domain containing 25) Enables DNA binding activity. Involved in positive regulation of cell motility. Located in endomembrane system. Is integral component of plasma 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=-0.74).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC25 | NM_018246.3 | c.*1884C>T | 3_prime_UTR_variant | 9/9 | ENST00000356537.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC25 | ENST00000356537.9 | c.*1884C>T | 3_prime_UTR_variant | 9/9 | 1 | NM_018246.3 | P1 | ||
CCDC25 | ENST00000520486.5 | c.*2330C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 1 | ||||
ENST00000521510.2 | n.647+771G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.424 AC: 64451AN: 151898Hom.: 14325 Cov.: 32
GnomAD3 genomes
?
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32
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GnomAD4 exome AF: 0.500 AC: 9AN: 18Hom.: 3 Cov.: 0 AF XY: 0.500 AC XY: 6AN XY: 12
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GnomAD4 genome ? AF: 0.424 AC: 64471AN: 152018Hom.: 14321 Cov.: 32 AF XY: 0.426 AC XY: 31678AN XY: 74322
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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