chr11-6271607-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001363552.2(CCKBR):​c.*64C>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 0.00000077 in 1,298,864 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.7e-7 (0 hom.)
• Consequence: CCKBR NM_001363552.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363552.2. 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.*64C>T		3_prime_UTR	Exon 5 of 5	NP_795344.1
	CCKBR	NM_001363552.2		c.*64C>T		3_prime_UTR	Exon 4 of 4	NP_001350481.1
	CCKBR	NM_001318029.2		c.*64C>T		3_prime_UTR	Exon 4 of 4	NP_001304958.1

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.70e-7 AC: 1 AN: 1298864 Hom.: 0 Cov.: 20 AF XY: 0.00000157 AC XY: 1 AN XY: 636992

African (AFR) AF: 0.00 AC: 0 AN: 29088

American (AMR) AF: 0.00 AC: 0 AN: 27142

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19482

East Asian (EAS) AF: 0.00 AC: 0 AN: 38012

South Asian (SAS) AF: 0.0000145 AC: 1 AN: 68768

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5210

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1022324

Other (OTH) AF: 0.00 AC: 0 AN: 54240

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.58
PhyloP100		-0.30

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;