chr11-6271607-C-G

Variant names:

• chr11-6271607-C-G
• rs10839535
• NM_176875.4:c.*64C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_176875.4(CCKBR):​c.*64C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 1,449,788 control chromosomes in the GnomAD database, including 521,234 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 0.80 (49707 hom., cov: 32)
  • Exomes 𝑓: 0.85 (471527 hom.)
• Consequence: CCKBR NM_176875.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_176875.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCKBR	NM_176875.4	MANE Select	c.*64C>G		3_prime_UTR	Exon 5 of 5	NP_795344.1	P32239-1
	CCKBR	NM_001363552.2		c.*64C>G		3_prime_UTR	Exon 4 of 4	NP_001350481.1	P32239-2
	CCKBR	NM_001318029.2		c.*64C>G		3_prime_UTR	Exon 4 of 4	NP_001304958.1	E9PIC8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCKBR	ENST00000334619.7	TSL:1 MANE Select	c.*64C>G		3_prime_UTR	Exon 5 of 5	ENSP00000335544.2	P32239-1
	CCKBR	ENST00000525462.1	TSL:1	c.*64C>G		3_prime_UTR	Exon 4 of 4	ENSP00000435534.1	P32239-2
	CCKBR	ENST00000912313.1		c.*64C>G		3_prime_UTR	Exon 5 of 5	ENSP00000582372.1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122008 AN: 151714 Hom.: 49678 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.819

GnomAD4 exome AF: 0.851 AC: 1105121 AN: 1297956 Hom.: 471527 Cov.: 20 AF XY: 0.851 AC XY: 541945 AN XY: 636526

African (AFR) AF: 0.663 AC: 19271 AN: 29070

American (AMR) AF: 0.887 AC: 24058 AN: 27136

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 16976 AN: 19474

East Asian (EAS) AF: 0.942 AC: 35798 AN: 38010

South Asian (SAS) AF: 0.838 AC: 57573 AN: 68722

European-Finnish (FIN) AF: 0.895 AC: 30946 AN: 34588

Middle Eastern (MID) AF: 0.866 AC: 4511 AN: 5210

European-Non Finnish (NFE) AF: 0.851 AC: 869780 AN: 1021542

Other (OTH) AF: 0.852 AC: 46208 AN: 54204

GnomAD4 genome AF: 0.804 AC: 122083 AN: 151832 Hom.: 49707 Cov.: 32 AF XY: 0.807 AC XY: 59908 AN XY: 74218

African (AFR) AF: 0.663 AC: 27388 AN: 41294

American (AMR) AF: 0.855 AC: 13060 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3030 AN: 3456

East Asian (EAS) AF: 0.947 AC: 4889 AN: 5164

South Asian (SAS) AF: 0.834 AC: 4021 AN: 4822

European-Finnish (FIN) AF: 0.887 AC: 9399 AN: 10602

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57649 AN: 67914

Other (OTH) AF: 0.821 AC: 1731 AN: 2108

Alfa AF: 0.771 Hom.: 1713

Bravo AF: 0.796

Asia WGS AF: 0.877 AC: 3052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.47
PhyloP100		-0.30
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: rs10839535; hg19: chr11-6292837;