rs1800843

Variant names:

• chr11-6270835-C-A
• rs1800843
• ENST00000525462.1:c.843C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-6270835-C-A
• chr11-6270835-C-G
• chr11-6270835-C-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000525462.1(CCKBR):​c.843C>A​(p.Gly281Gly) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 12 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525462.1. 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
	CCKBR	NM_176875.4	MANE Select	c.811+32C>A		intron	N/A	NP_795344.1
	CCKBR	NM_001363552.2		c.843C>A	p.Gly281Gly	synonymous	Exon 4 of 4	NP_001350481.1
	CCKBR	NM_001318029.2		c.559+32C>A		intron	N/A	NP_001304958.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCKBR	ENST00000525462.1	TSL:1	c.843C>A	p.Gly281Gly	synonymous	Exon 4 of 4	ENSP00000435534.1
	CCKBR	ENST00000334619.7	TSL:1 MANE Select	c.811+32C>A		intron	N/A	ENSP00000335544.2
	CCKBR	ENST00000532396.1	TSL:1	n.43+17C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27952 AN: 151972 Hom.: 2692 Cov.: 33

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

GnomAD2 exomes AF: 0.159 AC: 39753 AN: 249900 AF XY: 0.162

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 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.: 37 AF XY: 0.182 AC XY: 132550 AN XY: 726914

African (AFR) AF: 0.207 AC: 6933 AN: 33476

American (AMR) AF: 0.117 AC: 5234 AN: 44684

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 4912 AN: 26124

East Asian (EAS) AF: 0.0255 AC: 1011 AN: 39698

South Asian (SAS) AF: 0.166 AC: 14316 AN: 86240

European-Finnish (FIN) AF: 0.145 AC: 7691 AN: 53124

Middle Eastern (MID) AF: 0.127 AC: 731 AN: 5762

European-Non Finnish (NFE) AF: 0.194 AC: 215130 AN: 1111764

Other (OTH) AF: 0.180 AC: 10889 AN: 60378

GnomAD4 genome AF: 0.184 AC: 27961 AN: 152090 Hom.: 2692 Cov.: 33 AF XY: 0.178 AC XY: 13260 AN XY: 74342

African (AFR) AF: 0.209 AC: 8663 AN: 41480

American (AMR) AF: 0.166 AC: 2541 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3470

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5172

South Asian (SAS) AF: 0.153 AC: 736 AN: 4816

European-Finnish (FIN) AF: 0.137 AC: 1445 AN: 10566

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13131 AN: 67968

Other (OTH) AF: 0.171 AC: 361 AN: 2116

Alfa AF: 0.181 Hom.: 3385

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.45
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1800843; hg19: chr11-6292065; COSMIC: COSV58100519; COSMIC: COSV58100519;