rs16872762
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134848.2(CCDC152):c.*42A>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 0.0216 in 1,543,092 control chromosomes in the GnomAD database, including 1,734 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 0.018 ( 143 hom., cov: 33)
Exomes 𝑓: 0.022 ( 1591 hom. )
Consequence
CCDC152
NM_001134848.2 3_prime_UTR
NM_001134848.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.457
Genes affected
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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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC152 | NM_001134848.2 | c.*42A>G | 3_prime_UTR_variant | 9/9 | ENST00000361970.10 | NP_001128320.1 | ||
CCDC152 | XM_047416584.1 | c.*42A>G | 3_prime_UTR_variant | 9/9 | XP_047272540.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC152 | ENST00000361970.10 | c.*42A>G | 3_prime_UTR_variant | 9/9 | 1 | NM_001134848.2 | ENSP00000354888 | P1 | ||
CCDC152 | ENST00000388827.4 | c.*42A>G | 3_prime_UTR_variant | 7/7 | 2 | ENSP00000373479 |
Frequencies
GnomAD3 genomes AF: 0.0179 AC: 2726AN: 152220Hom.: 143 Cov.: 33
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GnomAD3 exomes AF: 0.0432 AC: 6434AN: 149048Hom.: 479 AF XY: 0.0513 AC XY: 4045AN XY: 78840
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GnomAD4 exome AF: 0.0220 AC: 30655AN: 1390754Hom.: 1591 Cov.: 30 AF XY: 0.0262 AC XY: 17998AN XY: 685648
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GnomAD4 genome AF: 0.0179 AC: 2729AN: 152338Hom.: 143 Cov.: 33 AF XY: 0.0206 AC XY: 1533AN XY: 74488
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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