Genetic Variant CCNA2:c.-255G>A (chr4-121823883-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The NM_001237.5(CCNA2):c.-255G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 557,246 control chromosomes in the GnomAD database, including 39,192 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 0.30 ( 8351 hom., cov: 34)

Exomes 𝑓: 0.38 ( 30841 hom. )

Consequence

CCNA2
NM_001237.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.47

Variant links:

Genes affected

CCNA2 (HGNC:1578): (cyclin A2) The protein encoded by this gene belongs to the highly conserved cyclin family, whose members function as regulators of the cell cycle. This protein binds and activates cyclin-dependent kinase 2 and thus promotes transition through G1/S and G2/M. [provided by RefSeq, Aug 2016]

CCNA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.13).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNA2	NM_001237.5 link	c.-255G>A		5_prime_UTR_variant	Exon 1 of 8	ENST00000274026.10	NP_001228.2	P20248

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNA2	ENST00000274026.10 link	c.-255G>A		5_prime_UTR_variant	Exon 1 of 8	1	NM_001237.5	ENSP00000274026.5		P20248

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45619

AN:

152116

Hom.:

8344

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0779

Gnomad AMI

AF:

0.401

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.404

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.303

GnomAD4 exome

AF:

0.381

AC:

154373

AN:

405012

Hom.:

30841

Cov.:

AF XY:

0.379

AC XY:

79689

AN XY:

210456

show subpopulations

Gnomad4 AFR exome

AF:

0.0759

Gnomad4 AMR exome

AF:

0.448

Gnomad4 ASJ exome

AF:

0.342

Gnomad4 EAS exome

AF:

0.526

Gnomad4 SAS exome

AF:

0.331

Gnomad4 FIN exome

AF:

0.428

Gnomad4 NFE exome

AF:

0.379

Gnomad4 OTH exome

AF:

0.364

GnomAD4 genome

AF:

0.300

AC:

45634

AN:

152234

Hom.:

8351

Cov.:

AF XY:

0.304

AC XY:

22637

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0778

Gnomad4 AMR

AF:

0.406

Gnomad4 ASJ

AF:

0.355

Gnomad4 EAS

AF:

0.439

Gnomad4 SAS

AF:

0.339

Gnomad4 FIN

AF:

0.404

Gnomad4 NFE

AF:

0.378

Gnomad4 OTH

AF:

0.304

Alfa

AF:

0.198

Hom.:

481

Bravo

AF:

0.290

Asia WGS

AF:

0.363

AC:

1266

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.13

CADD

Benign

DANN

Uncertain

0.98

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over