ENST00000590083.5:c.*215C>T

Variant names:

• chr19-1230678-G-A
• rs36074840
• ENST00000590083.5:c.*215C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

ACMG classification

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: ENST00000590083.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	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
	CBARP	NM_152769.3		c.*215C>T		3_prime_UTR	Exon 9 of 9	NP_689982.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CBARP	ENST00000590083.5	TSL:1	c.*215C>T		3_prime_UTR	Exon 9 of 9	ENSP00000465260.1
	CBARP	ENST00000650044.2	MANE Select	c.1154+423C>T		intron	N/A	ENSP00000497208.1
	CBARP	ENST00000382477.6	TSL:5	c.1214+423C>T		intron	N/A	ENSP00000371917.2

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

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

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

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: 59 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17121 AN: 67982

Other (OTH) AF: 0.229 AC: 484 AN: 2114

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
DANN	Benign	0.69
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs36074840; hg19: chr19-1230677;