rs4855656

chr3-108587728-G-A

Variant summary

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

The NM_020890.3(CIP2A):c.102+1546C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 152,164 control chromosomes in the GnomAD database, including 422 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 0.036 (422 hom., cov: 32)
• Consequence: CIP2A NM_020890.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CIP2A	NM_020890.3	c.102+1546C>T		intron_variant		ENST00000295746.13
CIP2A	XM_006713716.4	c.102+1546C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIP2A	ENST00000295746.13	c.102+1546C>T		intron_variant		1	NM_020890.3	P1

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5435 AN: 152048 Hom.: 421 Cov.: 32

Gnomad AFR AF: 0.00553

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0357 AC: 5439 AN: 152164 Hom.: 422 Cov.: 32 AF XY: 0.0410 AC XY: 3047 AN XY: 74394

Gnomad4 AFR AF: 0.00551

Gnomad4 AMR AF: 0.0716

Gnomad4 ASJ AF: 0.0430

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.0855

Gnomad4 FIN AF: 0.0517

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0384

Alfa AF: 0.0246 Hom.: 19

Bravo AF: 0.0376

Asia WGS AF: 0.204 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.20
Dann	Benign	0.70

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: rs4855656; hg19: chr3-108306575;