Variant 19-1229692-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001393918.1(CBARP):c.1605C>A(p.Arg535Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00449 in 1,053,050 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0048 ( 9 hom. )

Consequence

CBARP
NM_001393918.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.106

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 19-1229692-G-T is Benign according to our data. Variant chr19-1229692-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648908.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.106 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CBARP	NM_001393918.1 linkuse as main transcript	c.1605C>A	p.Arg535Arg	synonymous_variant	10/10	ENST00000650044.2	NP_001380847.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CBARP	ENST00000650044.2 linkuse as main transcript	c.1605C>A	p.Arg535Arg	synonymous_variant	10/10		NM_001393918.1	ENSP00000497208.1		Q8N350-3

Frequencies

GnomAD3 genomes

AF:

0.00227

AC:

331

AN:

145806

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000885

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00184

Gnomad ASJ

AF:

0.000295

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000418

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00399

Gnomad OTH

AF:

0.00150

GnomAD3 exomes

AF:

0.00248

AC:

AN:

20942

Hom.:

AF XY:

0.00255

AC XY:

AN XY:

13704

show subpopulations

Gnomad AFR exome

AF:

0.00556

Gnomad AMR exome

AF:

0.00278

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000667

Gnomad FIN exome

AF:

0.000536

Gnomad NFE exome

AF:

0.00496

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00484

AC:

4393

AN:

907256

Hom.:

Cov.:

AF XY:

0.00476

AC XY:

2061

AN XY:

432706

show subpopulations

Gnomad4 AFR exome

AF:

0.000365

Gnomad4 AMR exome

AF:

0.00158

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000353

Gnomad4 FIN exome

AF:

0.000193

Gnomad4 NFE exome

AF:

0.00530

Gnomad4 OTH exome

AF:

0.00440

GnomAD4 genome

AF:

0.00227

AC:

331

AN:

145794

Hom.:

Cov.:

AF XY:

0.00223

AC XY:

158

AN XY:

70852

show subpopulations

Gnomad4 AFR

AF:

0.000884

Gnomad4 AMR

AF:

0.00184

Gnomad4 ASJ

AF:

0.000295

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000420

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00399

Gnomad4 OTH

AF:

0.00149

Alfa

AF:

0.000957

Hom.:

Bravo

AF:

0.00225

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2022

CBARP: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.89

DANN

Benign

0.92

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