Variant rs1800843 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000525462.1(CCKBR):c.843C>A(p.Gly281=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,613,340 control chromosomes in the GnomAD database, including 28,075 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 0.18 ( 2692 hom., cov: 33)

Exomes 𝑓: 0.18 ( 25383 hom. )

Consequence

CCKBR
ENST00000525462.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.495

Variant links:

Genes affected

CCKBR (HGNC:1571): (cholecystokinin B receptor) This gene encodes a G-protein coupled receptor for gastrin and cholecystokinin (CCK), regulatory peptides of the brain and gastrointestinal tract. This protein is a type B gastrin receptor, which has a high affinity for both sulfated and nonsulfated CCK analogs and is found principally in the central nervous system and the gastrointestinal tract. Alternative splicing results in multiple transcript variants. A misspliced transcript variant including an intron has been observed in cells from colorectal and pancreatic tumors. [provided by RefSeq, Dec 2015]

CCKBR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP7

Synonymous conserved (PhyloP=-0.495 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CCKBR	NM_176875.4 linkuse as main transcript	c.811+32C>A		intron_variant		ENST00000334619.7	NP_795344.1
CCKBR	NM_001363552.2 linkuse as main transcript	c.843C>A	p.Gly281=	synonymous_variant	4/4		NP_001350481.1
CCKBR	NM_001318029.2 linkuse as main transcript	c.559+32C>A		intron_variant			NP_001304958.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCKBR	ENST00000525462.1 linkuse as main transcript	c.843C>A	p.Gly281=	synonymous_variant	4/4	1		ENSP00000435534		P32239-2
CCKBR	ENST00000334619.7 linkuse as main transcript	c.811+32C>A		intron_variant		1	NM_176875.4	ENSP00000335544	P1	P32239-1
CCKBR	ENST00000532396.1 linkuse as main transcript	n.43+17C>A		intron_variant, non_coding_transcript_variant		1
CCKBR	ENST00000532715.5 linkuse as main transcript	c.559+32C>A		intron_variant		3		ENSP00000432079

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

27952

AN:

151972

Hom.:

2692

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.166

Gnomad ASJ

AF:

0.178

Gnomad EAS

AF:

0.0218

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.169

GnomAD3 exomes

AF:

0.159

AC:

39753

AN:

249900

Hom.:

3463

AF XY:

0.162

AC XY:

21864

AN XY:

135156

show subpopulations

Gnomad AFR exome

AF:

0.212

Gnomad AMR exome

AF:

0.110

Gnomad ASJ exome

AF:

0.187

Gnomad EAS exome

AF:

0.0175

Gnomad SAS exome

AF:

0.163

Gnomad FIN exome

AF:

0.144

Gnomad NFE exome

AF:

0.189

Gnomad OTH exome

AF:

0.163

GnomAD4 exome

AF:

0.183

AC:

266847

AN:

1461250

Hom.:

25383

Cov.:

AF XY:

0.182

AC XY:

132550

AN XY:

726914

show subpopulations

Gnomad4 AFR exome

AF:

0.207

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.188

Gnomad4 EAS exome

AF:

0.0255

Gnomad4 SAS exome

AF:

0.166

Gnomad4 FIN exome

AF:

0.145

Gnomad4 NFE exome

AF:

0.194

Gnomad4 OTH exome

AF:

0.180

GnomAD4 genome

AF:

0.184

AC:

27961

AN:

152090

Hom.:

2692

Cov.:

AF XY:

0.178

AC XY:

13260

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.209

Gnomad4 AMR

AF:

0.166

Gnomad4 ASJ

AF:

0.178

Gnomad4 EAS

AF:

0.0215

Gnomad4 SAS

AF:

0.153

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.193

Gnomad4 OTH

AF:

0.171

Alfa

AF:

0.127

Hom.:

271

Bravo

AF:

0.186

Asia WGS

AF:

0.130

AC:

451

AN:

3478

EpiCase

AF:

0.191

EpiControl

AF:

0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.51

DANN

Benign

0.45

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over