NM_020313.4:c.9T>G

Variant names:

• chr16-57440920-A-C
• NM_020313.4:c.9T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_020313.4(CIAPIN1):​c.9T>G​(p.Asp3Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CIAPIN1 NM_020313.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.34
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.026295185).
• BP6: Variant 16-57440920-A-C is Benign according to our data. Variant chr16-57440920-A-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3492859.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020313.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIAPIN1	NM_020313.4	MANE Select	c.9T>G	p.Asp3Glu	missense	Exon 2 of 9	NP_064709.2	Q6FI81-1
	CIAPIN1	NM_001308347.2		c.9T>G	p.Asp3Glu	missense	Exon 2 of 9	NP_001295276.1	Q6FI81-3
	CIAPIN1	NM_001308358.2		c.9T>G	p.Asp3Glu	missense	Exon 2 of 8	NP_001295287.1	H3BT65

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIAPIN1	ENST00000394391.9	TSL:1 MANE Select	c.9T>G	p.Asp3Glu	missense	Exon 2 of 9	ENSP00000377914.4	Q6FI81-1
	CIAPIN1	ENST00000567518.5	TSL:1	c.9T>G	p.Asp3Glu	missense	Exon 2 of 9	ENSP00000456114.1	Q6FI81-3
	CIAPIN1	ENST00000939128.1		c.9T>G	p.Asp3Glu	missense	Exon 2 of 9	ENSP00000609187.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.2
DANN	Benign	0.71
DEOGEN2	Benign	0.048	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.023	N
LIST_S2	Benign	0.64	T
M_CAP	Benign	0.0016	T
MetaRNN	Benign	0.026	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.10	N
PhyloP100		-1.3
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-0.93	N
REVEL	Benign	0.072
Sift	Benign	0.42	T
Sift4G	Benign	0.33	T
Polyphen		0.0	B
Vest4		0.026
MutPred		0.23		Gain of sheet (P = 0.0477)
MVP		0.11
MPC		0.20
ClinPred		0.047	T
GERP RS		-11
PromoterAI		0.015	Neutral
Varity_R		0.059
gMVP		0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr16-57474832;