3-108552364-T-C

Variant names:

• chr3-108552364-T-C
• rs1033155512
• NM_020890.3:c.2417A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020890.3(CIP2A):​c.2417A>G​(p.Gln806Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CIP2A NM_020890.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.61

Genes affected

CIP2A (HGNC:29302): (cellular inhibitor of PP2A) Enables protein homodimerization activity. Predicted to act upstream of or within positive regulation of neural precursor cell proliferation and spermatogenesis. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1973423).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIP2A	NM_020890.3	c.2417A>G	p.Gln806Arg	missense_variant	Exon 20 of 21	ENST00000295746.13	NP_065941.2
CIP2A	XM_006713716.4	c.2414A>G	p.Gln805Arg	missense_variant	Exon 20 of 21		XP_006713779.1
CIP2A	XM_011513057.3	c.1475A>G	p.Gln492Arg	missense_variant	Exon 13 of 14		XP_011511359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIP2A	ENST00000295746.13	c.2417A>G	p.Gln806Arg	missense_variant	Exon 20 of 21	1	NM_020890.3	ENSP00000295746.7
CIP2A	ENST00000491772.5	c.1940A>G	p.Gln647Arg	missense_variant	Exon 20 of 21	1		ENSP00000419487.1
CIP2A	ENST00000481530.5	n.*1987A>G		non_coding_transcript_exon_variant	Exon 20 of 21	1		ENSP00000417297.1
CIP2A	ENST00000481530.5	n.*1987A>G		3_prime_UTR_variant	Exon 20 of 21	1		ENSP00000417297.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000362 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.094	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0060	T;.;T
Eigen	Benign	-0.054
Eigen_PC	Benign	0.055
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.69	T;T;T
M_CAP	Benign	0.023	T
MetaRNN	Benign	0.20	T;T;T
MetaSVM	Benign	-0.80	T
MutationAssessor	Benign	1.8	L;.;.
PrimateAI	Benign	0.41	T
PROVEAN	Benign	-0.83	N;N;.
REVEL	Benign	0.059
Sift	Benign	0.074	T;T;.
Sift4G	Benign	0.46	T;T;T
Polyphen		0.22	B;.;.
Vest4		0.37
MVP		0.65
MPC		0.28
ClinPred		0.66	D
GERP RS		4.7
Varity_R		0.20
gMVP		0.099

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: rs1033155512; hg19: chr3-108271211;