chr16-57447089-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_020313.4(CIAPIN1):c.-56+253C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0273 in 152,306 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.027 ( 81 hom., cov: 32)
Consequence
CIAPIN1
NM_020313.4 intron
NM_020313.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.186
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 16-57447089-G-A is Benign according to our data. Variant chr16-57447089-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1193917.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0273 (4158/152306) while in subpopulation NFE AF= 0.0353 (2399/68026). AF 95% confidence interval is 0.0341. There are 81 homozygotes in gnomad4. There are 1930 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 81 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIAPIN1 | NM_020313.4 | c.-56+253C>T | intron_variant | ENST00000394391.9 | |||
CIAPIN1 | NM_001308347.2 | c.-56+253C>T | intron_variant | ||||
CIAPIN1 | NM_001308358.2 | c.-56+253C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIAPIN1 | ENST00000394391.9 | c.-56+253C>T | intron_variant | 1 | NM_020313.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0274 AC: 4163AN: 152188Hom.: 81 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0273 AC: 4158AN: 152306Hom.: 81 Cov.: 32 AF XY: 0.0259 AC XY: 1930AN XY: 74474
GnomAD4 genome
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at