rs4518200

Variant names:

• chr4-163333270-C-A
• rs4518200
• ENST00000511901.1:c.-151-6565G>T

Variant summary

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

The ENST00000511901.1(NPY1R):​c.-151-6565G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 151,464 control chromosomes in the GnomAD database, including 57,157 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 0.87 (57157 hom., cov: 26)
• Consequence: NPY1R ENST00000511901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 8 publications found

Genes affected

NPY1R (HGNC:7956): (neuropeptide Y receptor Y1) This gene belongs to the G-protein-coupled receptor superfamily. The encoded transmembrane protein mediates the function of neuropeptide Y (NPY), a neurotransmitter, and peptide YY (PYY), a gastrointestinal hormone. The encoded receptor undergoes fast agonist-induced internalization through clathrin-coated pits and is subsequently recycled back to the cell membrane. Activation of Y1 receptors may result in mobilization of intracellular calcium and inhibition of adenylate cyclase activity. [provided by RefSeq, Aug 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY1R	XM_005263031.5	c.-151-6565G>T		intron_variant	Intron 1 of 2		XP_005263088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY1R	ENST00000511901.1	c.-151-6565G>T		intron_variant	Intron 1 of 1	3		ENSP00000423878.1

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131034 AN: 151346 Hom.: 57149 Cov.: 26

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.865 AC: 131083 AN: 151464 Hom.: 57157 Cov.: 26 AF XY: 0.869 AC XY: 64246 AN XY: 73960

African (AFR) AF: 0.747 AC: 30716 AN: 41146

American (AMR) AF: 0.906 AC: 13781 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3060 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5104 AN: 5142

South Asian (SAS) AF: 0.913 AC: 4302 AN: 4712

European-Finnish (FIN) AF: 0.919 AC: 9697 AN: 10550

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61522 AN: 67928

Other (OTH) AF: 0.856 AC: 1801 AN: 2104

Alfa AF: 0.891 Hom.: 44581

Bravo AF: 0.860

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		1.6
PromoterAI		-0.0076	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4518200; hg19: chr4-164254422;