chr16-57447393-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The ENST00000567518.5(CIAPIN1):c.-107A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 1,043,646 control chromosomes in the GnomAD database, including 294,655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.78 ( 47403 hom., cov: 35)
Exomes 𝑓: 0.74 ( 247252 hom. )
Consequence
CIAPIN1
ENST00000567518.5 5_prime_UTR
ENST00000567518.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.31
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 16-57447393-T-C is Benign according to our data. Variant chr16-57447393-T-C is described in ClinVar as [Benign]. Clinvar id is 1291333.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIAPIN1 | NM_020313.4 | upstream_gene_variant | ENST00000394391.9 | ||||
CIAPIN1 | NM_001308347.2 | upstream_gene_variant | |||||
CIAPIN1 | NM_001308358.2 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIAPIN1 | ENST00000394391.9 | upstream_gene_variant | 1 | NM_020313.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.782 AC: 118926AN: 152070Hom.: 47351 Cov.: 35
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GnomAD4 exome AF: 0.742 AC: 661396AN: 891458Hom.: 247252 Cov.: 12 AF XY: 0.742 AC XY: 316311AN XY: 426168
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GnomAD4 genome ? AF: 0.782 AC: 119040AN: 152188Hom.: 47403 Cov.: 35 AF XY: 0.775 AC XY: 57686AN XY: 74402
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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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