14-104880392-A-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001112726.3(CEP170B):āc.439A>Cā(p.Arg147=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,612,588 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0054 ( 9 hom., cov: 33)
Exomes š: 0.00081 ( 15 hom. )
Consequence
CEP170B
NM_001112726.3 synonymous
NM_001112726.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.50
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 14-104880392-A-C is Benign according to our data. Variant chr14-104880392-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 787955.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=3.5 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00543 (826/152178) while in subpopulation AFR AF= 0.0182 (755/41496). AF 95% confidence interval is 0.0171. There are 9 homozygotes in gnomad4. There are 382 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP170B | NM_001112726.3 | c.439A>C | p.Arg147= | synonymous_variant | 6/19 | ENST00000414716.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP170B | ENST00000414716.8 | c.439A>C | p.Arg147= | synonymous_variant | 6/19 | 1 | NM_001112726.3 | P1 | |
CEP170B | ENST00000556508.5 | c.229A>C | p.Arg77= | synonymous_variant | 5/18 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00541 AC: 823AN: 152060Hom.: 9 Cov.: 33
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GnomAD3 exomes AF: 0.00142 AC: 352AN: 247046Hom.: 3 AF XY: 0.00123 AC XY: 166AN XY: 134566
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GnomAD4 exome AF: 0.000808 AC: 1180AN: 1460410Hom.: 15 Cov.: 32 AF XY: 0.000772 AC XY: 561AN XY: 726466
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GnomAD4 genome AF: 0.00543 AC: 826AN: 152178Hom.: 9 Cov.: 33 AF XY: 0.00513 AC XY: 382AN XY: 74416
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 03, 2017 | - - |
CEP170B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 21, 2019 | This variant is classified as likely 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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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