chr14-104880295-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001112726.3(CEP170B):c.342G>A(p.Lys114=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0341 in 1,600,126 control chromosomes in the GnomAD database, including 1,085 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.029 ( 76 hom., cov: 33)
Exomes 𝑓: 0.035 ( 1009 hom. )
Consequence
CEP170B
NM_001112726.3 synonymous
NM_001112726.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.55
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=-0.45).
BP6
Variant 14-104880295-G-A is Benign according to our data. Variant chr14-104880295-G-A is described in ClinVar as [Benign]. Clinvar id is 3056165.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0286 (4350/152206) while in subpopulation SAS AF= 0.0441 (213/4832). AF 95% confidence interval is 0.0392. There are 76 homozygotes in gnomad4. There are 2158 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 76 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP170B | NM_001112726.3 | c.342G>A | p.Lys114= | synonymous_variant | 6/19 | ENST00000414716.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP170B | ENST00000414716.8 | c.342G>A | p.Lys114= | synonymous_variant | 6/19 | 1 | NM_001112726.3 | P1 | |
CEP170B | ENST00000556508.5 | c.132G>A | p.Lys44= | synonymous_variant | 5/18 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0286 AC: 4355AN: 152088Hom.: 77 Cov.: 33
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GnomAD3 exomes AF: 0.0340 AC: 7691AN: 226382Hom.: 155 AF XY: 0.0353 AC XY: 4345AN XY: 123080
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GnomAD4 exome AF: 0.0347 AC: 50213AN: 1447920Hom.: 1009 Cov.: 32 AF XY: 0.0353 AC XY: 25365AN XY: 718998
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GnomAD4 genome AF: 0.0286 AC: 4350AN: 152206Hom.: 76 Cov.: 33 AF XY: 0.0290 AC XY: 2158AN XY: 74416
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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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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