14-104878486-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001112726.3(CEP170B):c.318G>A(p.Pro106=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0343 in 1,611,574 control chromosomes in the GnomAD database, including 1,106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.029 ( 78 hom., cov: 33)
Exomes 𝑓: 0.035 ( 1028 hom. )
Consequence
CEP170B
NM_001112726.3 synonymous
NM_001112726.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.63
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 14-104878486-G-A is Benign according to our data. Variant chr14-104878486-G-A is described in ClinVar as [Benign]. Clinvar id is 3055708.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.63 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0288 (4390/152328) while in subpopulation SAS AF= 0.0434 (209/4820). AF 95% confidence interval is 0.0385. There are 78 homozygotes in gnomad4. There are 2174 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 78 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP170B | NM_001112726.3 | c.318G>A | p.Pro106= | synonymous_variant | 5/19 | ENST00000414716.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP170B | ENST00000414716.8 | c.318G>A | p.Pro106= | synonymous_variant | 5/19 | 1 | NM_001112726.3 | P1 | |
CEP170B | ENST00000556508.5 | c.108G>A | p.Pro36= | synonymous_variant | 4/18 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0289 AC: 4395AN: 152210Hom.: 79 Cov.: 33
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GnomAD3 exomes AF: 0.0345 AC: 8516AN: 246920Hom.: 174 AF XY: 0.0360 AC XY: 4833AN XY: 134426
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GnomAD4 exome AF: 0.0349 AC: 50939AN: 1459246Hom.: 1028 Cov.: 37 AF XY: 0.0355 AC XY: 25795AN XY: 725942
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GnomAD4 genome AF: 0.0288 AC: 4390AN: 152328Hom.: 78 Cov.: 33 AF XY: 0.0292 AC XY: 2174AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CEP170B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 27, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at