rs1530771
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152446.5(CEP128):c.2880+101G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 1,051,526 control chromosomes in the GnomAD database, including 154,935 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 0.57 ( 24601 hom., cov: 31)
Exomes 𝑓: 0.53 ( 130334 hom. )
Consequence
CEP128
NM_152446.5 intron
NM_152446.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.10
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP128 | NM_152446.5 | c.2880+101G>T | intron_variant | ENST00000555265.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP128 | ENST00000555265.6 | c.2880+101G>T | intron_variant | 5 | NM_152446.5 | P2 | |||
CEP128 | ENST00000281129.7 | c.2880+101G>T | intron_variant | 1 | P2 | ||||
CEP128 | ENST00000556061.5 | c.76+101G>T | intron_variant | 5 | |||||
CEP128 | ENST00000554502.5 | c.1955+101G>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.565 AC: 85788AN: 151766Hom.: 24550 Cov.: 31
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GnomAD4 exome AF: 0.534 AC: 480794AN: 899642Hom.: 130334 AF XY: 0.537 AC XY: 251885AN XY: 469362
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GnomAD4 genome AF: 0.566 AC: 85905AN: 151884Hom.: 24601 Cov.: 31 AF XY: 0.564 AC XY: 41886AN XY: 74224
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ClinVar
Not reported inComputational scores
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Name
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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