19-32881858-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_032816.5(CEP89):c.2121G>A(p.Ala707=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000393 in 1,602,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000039 ( 0 hom. )
Consequence
CEP89
NM_032816.5 synonymous
NM_032816.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.49
Genes affected
CEP89 (HGNC:25907): (centrosomal protein 89) Involved in non-motile cilium assembly. Acts upstream of or within cilium assembly. Located in several cellular components, including cytosol; microtubule cytoskeleton; and non-motile cilium. Part of ciliary transition fiber. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 19-32881858-C-T is Benign according to our data. Variant chr19-32881858-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2171099.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.49 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP89 | NM_032816.5 | c.2121G>A | p.Ala707= | synonymous_variant | 18/19 | ENST00000305768.10 | |
CEP89 | XM_005259344.4 | c.2049G>A | p.Ala683= | synonymous_variant | 18/19 | ||
CEP89 | XM_047439562.1 | c.1380G>A | p.Ala460= | synonymous_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP89 | ENST00000305768.10 | c.2121G>A | p.Ala707= | synonymous_variant | 18/19 | 1 | NM_032816.5 | P3 | |
CEP89 | ENST00000586984.6 | c.*730G>A | 3_prime_UTR_variant, NMD_transcript_variant | 17/18 | 1 | ||||
CEP89 | ENST00000591698.5 | c.*1455G>A | 3_prime_UTR_variant, NMD_transcript_variant | 17/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152230Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000756 AC: 18AN: 237946Hom.: 0 AF XY: 0.0000852 AC XY: 11AN XY: 129170
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GnomAD4 exome AF: 0.0000393 AC: 57AN: 1450428Hom.: 0 Cov.: 31 AF XY: 0.0000499 AC XY: 36AN XY: 721414
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74494
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2022 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at