16-57447393-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

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: 118926 AN: 152070 Hom.: 47351 Cov.: 35

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.783

GnomAD4 exome AF: 0.742 AC: 661396 AN: 891458 Hom.: 247252 Cov.: 12 AF XY: 0.742 AC XY: 316311 AN XY: 426168

Gnomad4 AFR exome AF: 0.943

Gnomad4 AMR exome AF: 0.631

Gnomad4 ASJ exome AF: 0.764

Gnomad4 EAS exome AF: 0.505

Gnomad4 SAS exome AF: 0.703

Gnomad4 FIN exome AF: 0.686

Gnomad4 NFE exome AF: 0.748

Gnomad4 OTH exome AF: 0.752

GnomAD4 genome AF: 0.782 AC: 119040 AN: 152188 Hom.: 47403 Cov.: 35 AF XY: 0.775 AC XY: 57686 AN XY: 74402

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.786

Alfa AF: 0.748 Hom.: 13209

Bravo AF: 0.786

Asia WGS AF: 0.694 AC: 2417 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	12
Dann	Benign	0.66

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

Other links and lift over

dbSNP: rs178602; hg19: chr16-57481305; COSMIC: COSV52646760; COSMIC: COSV52646760;