16-57447326-C-A

Variant summary

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

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

ACMG classification

Verdict is Benign. Variant got -12 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_single_submitter, 1 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/exons	MANE	UniProt
CIAPIN1	NM_020313.4	c.-56+16G>T		intron_variant		ENST00000394391.9
CIAPIN1	NM_001308347.2	c.-56+16G>T		intron_variant
CIAPIN1	NM_001308358.2	c.-56+16G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIAPIN1	ENST00000394391.9	c.-56+16G>T		intron_variant		1	NM_020313.4	P1

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12044 AN: 151442 Hom.: 863 Cov.: 32

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

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

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

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

Other links and lift over

dbSNP: rs11862474; hg19: chr16-57481238;