Genetic Variant CBARP:c.*215C>T (chr19-1230678-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152769.3(CBARP):c.*215C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,275,240 control chromosomes in the GnomAD database, including 43,822 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 0.22 ( 4155 hom., cov: 32)

Exomes 𝑓: 0.26 ( 39667 hom. )

Consequence

CBARP
NM_152769.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.124

Publications

5 publications found

Variant links:

Genes affected

CBARP (HGNC:28617): (CACN subunit beta associated regulatory protein) Predicted to enable transmembrane transporter binding activity. Predicted to be involved in negative regulation of calcium ion-dependent exocytosis and negative regulation of voltage-gated calcium channel activity. Predicted to be located in synaptic vesicle membrane. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. Predicted to colocalize with growth cone and secretory granule. [provided by Alliance of Genome Resources, Apr 2022]

CBARP links:

CBARP-DT (HGNC:55285): (CBARP divergent transcript)

CBARP-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152769.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CBARP	NM_001393918.1	MANE Select	c.1154+423C>T		intron	N/A	NP_001380847.1	Q8N350-3
	CBARP	NM_152769.3		c.*215C>T		3_prime_UTR	Exon 9 of 9	NP_689982.3	Q8N350-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CBARP	ENST00000590083.5	TSL:1	c.*215C>T	3_prime_UTR	Exon 9 of 9	ENSP00000465260.1	Q8N350-4
CBARP	ENST00000650044.2	MANE Select	c.1154+423C>T	intron	N/A	ENSP00000497208.1	Q8N350-3
CBARP	ENST00000917007.1		c.1358+219C>T	intron	N/A	ENSP00000587066.1

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33268

AN:

152088

Hom.:

4160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.287

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.230

GnomAD4 exome

AF:

0.261

AC:

293639

AN:

1123034

Hom.:

39667

Cov.:

AF XY:

0.261

AC XY:

139336

AN XY:

533926

show subpopulations

African (AFR)

AF:

0.101

AC:

2363

AN:

23332

American (AMR)

AF:

0.210

AC:

2402

AN:

11436

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

3228

AN:

15234

East Asian (EAS)

AF:

0.428

AC:

11423

AN:

26662

South Asian (SAS)

AF:

0.296

AC:

8867

AN:

30006

European-Finnish (FIN)

AF:

0.244

AC:

5670

AN:

23270

Middle Eastern (MID)

AF:

0.193

AC:

591

AN:

3064

European-Non Finnish (NFE)

AF:

0.262

AC:

247616

AN:

944268

Other (OTH)

AF:

0.251

AC:

11479

AN:

45762

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

12295

24591

36886

49182

61477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9588

19176

28764

38352

47940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.219

AC:

33270

AN:

152206

Hom.:

4155

Cov.:

AF XY:

0.222

AC XY:

16554

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.108

AC:

4502

AN:

41534

American (AMR)

AF:

0.234

AC:

3584

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

779

AN:

3472

East Asian (EAS)

AF:

0.458

AC:

2368

AN:

5166

South Asian (SAS)

AF:

0.330

AC:

1591

AN:

4824

European-Finnish (FIN)

AF:

0.238

AC:

2520

AN:

10606

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.252

AC:

17121

AN:

67982

Other (OTH)

AF:

0.229

AC:

484

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1312

2624

3936

5248

6560

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.222

Hom.:

499

Bravo

AF:

0.211

Asia WGS

AF:

0.365

AC:

1265

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.6

(source)

DANN

Benign

0.69

PhyloP100

0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over