3-42266417-G-T

Variant names:

• chr3-42266417-G-T
• rs13069836
• ENST00000631079.3:n.1504G>T

Variant summary

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

The ENST00000631079.3(ENSG00000281160):​n.1504G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,026 control chromosomes in the GnomAD database, including 22,211 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 0.54 (22209 hom., cov: 32)
  • Exomes 𝑓: 0.47 (2 hom.)
• Consequence: ENSG00000281160 ENST00000631079.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 5 publications found

Genes affected

ENSG00000281160 (HGNC:):

CCK (HGNC:1569): (cholecystokinin) This gene encodes a member of the gastrin/cholecystokinin family of proteins. The encoded preproprotein is proteolytically processed to generate multiple protein products, including the peptide hormones cholecystokinin-8, -12, -33, and others. The encoded peptides have been shown to regulate gastric acid secretion and food intake. A sulfated form of cholecystokinin-8 may modulate neuronal activity in the brain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631079.3. 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
	CCK	NM_000729.6	MANE Select	c.-1116C>A		upstream_gene	N/A	NP_000720.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000281160	ENST00000631079.3	TSL:6	n.1504G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000281160	ENST00000807313.1		n.1232+26G>T		intron	N/A
	CCK	ENST00000396169.7	TSL:1 MANE Select	c.-1116C>A		upstream_gene	N/A	ENSP00000379472.2

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81565 AN: 151886 Hom.: 22192 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.559

GnomAD4 exome AF: 0.467 AC: 14 AN: 30 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 11 AN XY: 22

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 4 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.400 AC: 8 AN: 20

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.537 AC: 81619 AN: 151996 Hom.: 22209 Cov.: 32 AF XY: 0.543 AC XY: 40327 AN XY: 74276

African (AFR) AF: 0.586 AC: 24295 AN: 41454

American (AMR) AF: 0.553 AC: 8443 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2277 AN: 3464

East Asian (EAS) AF: 0.559 AC: 2880 AN: 5152

South Asian (SAS) AF: 0.636 AC: 3064 AN: 4820

European-Finnish (FIN) AF: 0.544 AC: 5759 AN: 10578

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32979 AN: 67938

Other (OTH) AF: 0.560 AC: 1182 AN: 2110

Alfa AF: 0.532 Hom.: 3358

Bravo AF: 0.536

Asia WGS AF: 0.606 AC: 2094 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.48
PhyloP100		-0.44
PromoterAI		-0.0028	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13069836; hg19: chr3-42307909;