Genetic Variant NM_001393997.1:c.84C>T (chr8-22606110-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001393997.1(CCAR2):c.84C>T(p.Gly28Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,610,666 control chromosomes in the GnomAD database, including 82,545 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.30 ( 7230 hom., cov: 32)

Exomes 𝑓: 0.32 ( 75315 hom. )

Consequence

CCAR2
NM_001393997.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.00

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 8-22606110-C-T is Benign according to our data. Variant chr8-22606110-C-T is described in ClinVar as [Benign]. Clinvar id is 3059932.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCAR2	NM_001393997.1 link	c.84C>T	p.Gly28Gly	synonymous_variant	Exon 3 of 21	ENST00000308511.9	NP_001380926.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCAR2	ENST00000308511.9 link	c.84C>T	p.Gly28Gly	synonymous_variant	Exon 3 of 21	1	NM_001393997.1	ENSP00000310670.4		Q8N163-1

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

45946

AN:

151880

Hom.:

7225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.305

Gnomad EAS

AF:

0.197

Gnomad SAS

AF:

0.367

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.329

Gnomad OTH

AF:

0.299

GnomAD3 exomes

AF:

0.300

AC:

75312

AN:

251446

Hom.:

11681

AF XY:

0.306

AC XY:

41612

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.285

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.312

Gnomad EAS exome

AF:

0.192

Gnomad SAS exome

AF:

0.358

Gnomad FIN exome

AF:

0.261

Gnomad NFE exome

AF:

0.332

Gnomad OTH exome

AF:

0.304

GnomAD4 exome

AF:

0.319

AC:

465832

AN:

1458668

Hom.:

75315

Cov.:

AF XY:

0.322

AC XY:

233582

AN XY:

725864

show subpopulations

Gnomad4 AFR exome

AF:

0.284

Gnomad4 AMR exome

AF:

0.230

Gnomad4 ASJ exome

AF:

0.316

Gnomad4 EAS exome

AF:

0.227

Gnomad4 SAS exome

AF:

0.358

Gnomad4 FIN exome

AF:

0.260

Gnomad4 NFE exome

AF:

0.328

Gnomad4 OTH exome

AF:

0.316

GnomAD4 genome

AF:

0.302

AC:

45974

AN:

151998

Hom.:

7230

Cov.:

AF XY:

0.298

AC XY:

22128

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.290

Gnomad4 ASJ

AF:

0.305

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.367

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.329

Gnomad4 OTH

AF:

0.299

Alfa

AF:

0.328

Hom.:

13886

Bravo

AF:

0.299

Asia WGS

AF:

0.307

AC:

1066

AN:

3478

EpiCase

AF:

0.327

EpiControl

AF:

0.328

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CCAR2-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.65

CADD

Benign

5.1

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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