rs4518200

chr4-163333270-C-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NPY1R	XM_005263031.5	c.-151-6565G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPY1R	ENST00000511901.1	c.-151-6565G>T		intron_variant		3

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

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.856

Alfa AF: 0.892 Hom.: 31274

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4518200; hg19: chr4-164254422;