16-57447326-C-A
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_020313.4(CIAPIN1):c.-56+16G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 454,172 control chromosomes in the GnomAD database, including 1,241 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.080 ( 863 hom., cov: 32)
Exomes 𝑓: 0.039 ( 378 hom. )
Consequence
CIAPIN1
NM_020313.4 intron
NM_020313.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.60
Genes affected
CIAPIN1 (HGNC:28050): (cytokine induced apoptosis inhibitor 1) CIAPIN1 is a cytokine-induced inhibitor of apoptosis with no relation to apoptosis regulatory molecules of the BCL2 (MIM 151430) or CASP (see MIM 147678) families. Expression of CIAPIN1 is dependent on growth factor stimulation (Shibayama et al., 2004 [PubMed 14970183]).[supplied by OMIM, Mar 2008]
COQ9 (HGNC:25302): (coenzyme Q9) This locus represents a mitochondrial ubiquinone biosynthesis gene. The encoded protein is likely necessary for biosynthesis of coenzyme Q10, as mutations at this locus have been associated with autosomal-recessive neonatal-onset primary coenzyme Q10 deficiency.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 16-57447326-C-A is Benign according to our data. Variant chr16-57447326-C-A is described in ClinVar as [Benign]. Clinvar id is 1229725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CIAPIN1 | NM_020313.4 | c.-56+16G>T | intron_variant | Intron 1 of 8 | ENST00000394391.9 | NP_064709.2 | ||
CIAPIN1 | NM_001308347.2 | c.-56+16G>T | intron_variant | Intron 1 of 8 | NP_001295276.1 | |||
CIAPIN1 | NM_001308358.2 | c.-56+16G>T | intron_variant | Intron 1 of 7 | NP_001295287.1 | |||
COQ9 | NM_020312.4 | c.-180C>A | upstream_gene_variant | ENST00000262507.11 | NP_064708.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0795 AC: 12044AN: 151442Hom.: 863 Cov.: 32
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GnomAD4 exome AF: 0.0393 AC: 11896AN: 302612Hom.: 378 Cov.: 5 AF XY: 0.0390 AC XY: 5938AN XY: 152186
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GnomAD4 genome AF: 0.0796 AC: 12063AN: 151560Hom.: 863 Cov.: 32 AF XY: 0.0783 AC XY: 5803AN XY: 74126
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Jun 26, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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