12-94308613-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_016122.3(CEP83):c.*200T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00432 in 368,770 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0087 ( 25 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 4 hom. )
Consequence
CEP83
NM_016122.3 3_prime_UTR
NM_016122.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.255
Genes affected
CEP83 (HGNC:17966): (centrosomal protein 83) The protein encoded by this gene is a centriolar protein involved in primary cilium assembly. Defects in this gene have been associated with infantile nephronophthisis and intellectual disability. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 12-94308613-A-G is Benign according to our data. Variant chr12-94308613-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1338909.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00868 (1322/152298) while in subpopulation AFR AF= 0.0304 (1265/41576). AF 95% confidence interval is 0.029. There are 25 homozygotes in gnomad4. There are 623 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 26 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP83 | NM_016122.3 | c.*200T>C | 3_prime_UTR_variant | 17/17 | ENST00000397809.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP83 | ENST00000397809.10 | c.*200T>C | 3_prime_UTR_variant | 17/17 | 1 | NM_016122.3 | P1 | ||
CEP83 | ENST00000339839.9 | c.*200T>C | 3_prime_UTR_variant | 16/16 | 1 | P1 | |||
CEP83 | ENST00000552632.5 | c.*30+170T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00867 AC: 1319AN: 152180Hom.: 26 Cov.: 32
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GnomAD4 exome AF: 0.00125 AC: 270AN: 216472Hom.: 4 Cov.: 2 AF XY: 0.00109 AC XY: 122AN XY: 112110
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GnomAD4 genome ? AF: 0.00868 AC: 1322AN: 152298Hom.: 25 Cov.: 32 AF XY: 0.00837 AC XY: 623AN XY: 74468
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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 | GeneDx | May 16, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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