16-57447326-C-A

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.60
Variant links:
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]

Genome browser will be placed here

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
CIAPIN1NM_020313.4 linkc.-56+16G>T intron_variant Intron 1 of 8 ENST00000394391.9 NP_064709.2 Q6FI81-1
CIAPIN1NM_001308347.2 linkc.-56+16G>T intron_variant Intron 1 of 8 NP_001295276.1 Q6FI81-3
CIAPIN1NM_001308358.2 linkc.-56+16G>T intron_variant Intron 1 of 7 NP_001295287.1 Q6FI81H3BT65
COQ9NM_020312.4 linkc.-180C>A upstream_gene_variant ENST00000262507.11 NP_064708.1 O75208-1A0A024R6U3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CIAPIN1ENST00000394391.9 linkc.-56+16G>T intron_variant Intron 1 of 8 1 NM_020313.4 ENSP00000377914.4 Q6FI81-1
COQ9ENST00000262507.11 linkc.-180C>A upstream_gene_variant 1 NM_020312.4 ENSP00000262507.5 O75208-1

Frequencies

GnomAD3 genomes
AF:
0.0795
AC:
12044
AN:
151442
Hom.:
863
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0534
Gnomad ASJ
AF:
0.0628
Gnomad EAS
AF:
0.00627
Gnomad SAS
AF:
0.0719
Gnomad FIN
AF:
0.0216
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0342
Gnomad OTH
AF:
0.0766
GnomAD4 exome
AF:
0.0393
AC:
11896
AN:
302612
Hom.:
378
Cov.:
5
AF XY:
0.0390
AC XY:
5938
AN XY:
152186
show subpopulations
Gnomad4 AFR exome
AF:
0.190
Gnomad4 AMR exome
AF:
0.0472
Gnomad4 ASJ exome
AF:
0.0655
Gnomad4 EAS exome
AF:
0.000737
Gnomad4 SAS exome
AF:
0.0791
Gnomad4 FIN exome
AF:
0.0185
Gnomad4 NFE exome
AF:
0.0357
Gnomad4 OTH exome
AF:
0.0599
GnomAD4 genome
AF:
0.0796
AC:
12063
AN:
151560
Hom.:
863
Cov.:
32
AF XY:
0.0783
AC XY:
5803
AN XY:
74126
show subpopulations
Gnomad4 AFR
AF:
0.193
Gnomad4 AMR
AF:
0.0532
Gnomad4 ASJ
AF:
0.0628
Gnomad4 EAS
AF:
0.00629
Gnomad4 SAS
AF:
0.0721
Gnomad4 FIN
AF:
0.0216
Gnomad4 NFE
AF:
0.0342
Gnomad4 OTH
AF:
0.0758
Alfa
AF:
0.0339
Hom.:
64
Bravo
AF:
0.0869
Asia WGS
AF:
0.0600
AC:
208
AN:
3478

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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
CADD
Benign
6.0
DANN
Benign
0.43
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11862474; hg19: chr16-57481238; API