rs36074840

chr19-1230678-G-Achr19-1230678-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000590083.5(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 ENST00000590083.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CBARP	NM_001393918.1	c.1154+423C>T		intron_variant		ENST00000650044.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CBARP	ENST00000650044.2	c.1154+423C>T		intron_variant			NM_001393918.1	A2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33268 AN: 152088 Hom.: 4160 Cov.: 32

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.: 32 AF XY: 0.261 AC XY: 139336 AN XY: 533926

Gnomad4 AFR exome AF: 0.101

Gnomad4 AMR exome AF: 0.210

Gnomad4 ASJ exome AF: 0.212

Gnomad4 EAS exome AF: 0.428

Gnomad4 SAS exome AF: 0.296

Gnomad4 FIN exome AF: 0.244

Gnomad4 NFE exome AF: 0.262

Gnomad4 OTH exome AF: 0.251

GnomAD4 genome AF: 0.219 AC: 33270 AN: 152206 Hom.: 4155 Cov.: 32 AF XY: 0.222 AC XY: 16554 AN XY: 74414

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.229

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.6
Dann	Benign	0.69

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

Other links and lift over

dbSNP: rs36074840; hg19: chr19-1230677;