chr4-26485287-A-G

Variant names:

• chr4-26485287-A-G
• rs7665027
• NM_000730.3:c.626+350T>C

Variant summary

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

The NM_000730.3(CCKAR):​c.626+350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,160 control chromosomes in the GnomAD database, including 2,097 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 0.16 (2097 hom., cov: 32)
• Consequence: CCKAR NM_000730.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 9 publications found

Genes affected

CCKAR (HGNC:1570): (cholecystokinin A receptor) This gene encodes a G-protein coupled receptor that binds non-sulfated members of the cholecystokinin (CCK) family of peptide hormones. This receptor is a major physiologic mediator of pancreatic enzyme secretion and smooth muscle contraction of the gallbladder and stomach. In the central and peripheral nervous system this receptor regulates satiety and the release of beta-endorphin and dopamine. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000730.3. 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
	CCKAR	NM_000730.3	MANE Select	c.626+350T>C		intron	N/A	NP_000721.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCKAR	ENST00000295589.4	TSL:1 MANE Select	c.626+350T>C		intron	N/A	ENSP00000295589.3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24239 AN: 152048 Hom.: 2098 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.167

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.159 AC: 24244 AN: 152160 Hom.: 2097 Cov.: 32 AF XY: 0.160 AC XY: 11871 AN XY: 74388

African (AFR) AF: 0.181 AC: 7531 AN: 41506

American (AMR) AF: 0.126 AC: 1930 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1235 AN: 5162

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4820

European-Finnish (FIN) AF: 0.0997 AC: 1055 AN: 10586

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9634 AN: 68012

Other (OTH) AF: 0.165 AC: 349 AN: 2114

Alfa AF: 0.150 Hom.: 7934

Bravo AF: 0.158

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.019
DANN	Benign	0.44
PhyloP100		-0.066
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: rs7665027; hg19: chr4-26486909;