Variant 8-22614311-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001393997.1(CCAR2):c.924G>A(p.Ser308=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,613,598 control chromosomes in the GnomAD database, including 80,052 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5849 hom., cov: 32)

Exomes 𝑓: 0.32 ( 74203 hom. )

Consequence

CCAR2
NM_001393997.1 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.281

Variant links:

Genes affected

CCAR2 (HGNC:23360): (cell cycle and apoptosis regulator 2) Enables RNA polymerase II complex binding activity and enzyme inhibitor activity. Involved in several processes, including regulation of cellular protein metabolic process; regulation of signal transduction; and regulation of transcription, DNA-templated. Located in several cellular components, including mitochondrial matrix; nucleoplasm; and spindle. Part of DBIRD complex. [provided by Alliance of Genome Resources, Apr 2022]

CCAR2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 8-22614311-G-A is Benign according to our data. Variant chr8-22614311-G-A is described in ClinVar as [Benign]. Clinvar id is 3060085.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.281 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCAR2	NM_001393997.1 linkuse as main transcript	c.924G>A	p.Ser308=	synonymous_variant	9/21	ENST00000308511.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCAR2	ENST00000308511.9 linkuse as main transcript	c.924G>A	p.Ser308=	synonymous_variant	9/21	1	NM_001393997.1	P1	Q8N163-1
	ENST00000521025.1 linkuse as main transcript	n.2347C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

40018

AN:

152042

Hom.:

5847

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.369

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.269

GnomAD3 exomes

AF:

0.292

AC:

73224

AN:

250914

Hom.:

11180

AF XY:

0.301

AC XY:

40882

AN XY:

135652

show subpopulations

Gnomad AFR exome

AF:

0.137

Gnomad AMR exome

AF:

0.213

Gnomad ASJ exome

AF:

0.312

Gnomad EAS exome

AF:

0.251

Gnomad SAS exome

AF:

0.359

Gnomad FIN exome

AF:

0.261

Gnomad NFE exome

AF:

0.330

Gnomad OTH exome

AF:

0.296

GnomAD4 exome

AF:

0.316

AC:

462166

AN:

1461438

Hom.:

74203

Cov.:

AF XY:

0.319

AC XY:

232098

AN XY:

727000

show subpopulations

Gnomad4 AFR exome

AF:

0.134

Gnomad4 AMR exome

AF:

0.218

Gnomad4 ASJ exome

AF:

0.316

Gnomad4 EAS exome

AF:

0.293

Gnomad4 SAS exome

AF:

0.359

Gnomad4 FIN exome

AF:

0.260

Gnomad4 NFE exome

AF:

0.327

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.263

AC:

40020

AN:

152160

Hom.:

5849

Cov.:

AF XY:

0.261

AC XY:

19384

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.142

Gnomad4 AMR

AF:

0.267

Gnomad4 ASJ

AF:

0.306

Gnomad4 EAS

AF:

0.257

Gnomad4 SAS

AF:

0.370

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.327

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.306

Hom.:

10993

Bravo

AF:

0.253

Asia WGS

AF:

0.317

AC:

1101

AN:

3478

EpiCase

AF:

0.325

EpiControl

AF:

0.327

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

CCAR2-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.84

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over