16-57447089-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

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

ACMG classification

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: 4163 AN: 152188 Hom.: 81 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0211

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0189

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0353

Gnomad OTH AF: 0.0339

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0273 AC: 4158 AN: 152306 Hom.: 81 Cov.: 32 AF XY: 0.0259 AC XY: 1930 AN XY: 74474

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0211

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.0189

Gnomad4 NFE AF: 0.0353

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0281 Hom.: 6

Bravo AF: 0.0275

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	6.3
Dann	Benign	0.69

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: rs223860; hg19: chr16-57481001;