chr4-26485287-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0660
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCKARNM_000730.3 linkuse as main transcriptc.626+350T>C intron_variant ENST00000295589.4 NP_000721.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCKARENST00000295589.4 linkuse as main transcriptc.626+350T>C intron_variant 1 NM_000730.3 ENSP00000295589 P1

Frequencies

GnomAD3 genomes
AF:
0.159
AC:
24239
AN:
152048
Hom.:
2098
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.181
Gnomad4 AMR
AF:
0.126
Gnomad4 ASJ
AF:
0.277
Gnomad4 EAS
AF:
0.239
Gnomad4 SAS
AF:
0.306
Gnomad4 FIN
AF:
0.0997
Gnomad4 NFE
AF:
0.142
Gnomad4 OTH
AF:
0.165
Alfa
AF:
0.150
Hom.:
3771
Bravo
AF:
0.158
Asia WGS
AF:
0.238
AC:
828
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.019
DANN
Benign
0.44

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7665027; hg19: chr4-26486909; API