rs16957051

chr16-57434496-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020313.4(CIAPIN1):c.388-284A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,192 control chromosomes in the GnomAD database, including 578 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.068 (578 hom., cov: 33)
• Consequence: CIAPIN1 NM_020313.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CIAPIN1	NM_020313.4	c.388-284A>G		intron_variant		ENST00000394391.9
CIAPIN1	NM_001308347.2	c.349-284A>G		intron_variant
CIAPIN1	NM_001308358.2	c.388-284A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIAPIN1	ENST00000394391.9	c.388-284A>G		intron_variant		1	NM_020313.4	P1

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10295 AN: 152074 Hom.: 579 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.00616

Gnomad SAS AF: 0.0716

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0677 AC: 10307 AN: 152192 Hom.: 578 Cov.: 33 AF XY: 0.0667 AC XY: 4962 AN XY: 74416

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0487

Gnomad4 ASJ AF: 0.0629

Gnomad4 EAS AF: 0.00618

Gnomad4 SAS AF: 0.0719

Gnomad4 FIN AF: 0.0217

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0473 Hom.: 59

Bravo AF: 0.0730

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.0
Dann	Benign	0.75

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: rs16957051; hg19: chr16-57468408;