rs4234955

chr4-163339124-G-Achr4-163339124-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511901.1(NPY1R):c.-152+5181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,006 control chromosomes in the GnomAD database, including 31,762 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 0.62 (31762 hom., cov: 31)
• Consequence: NPY1R ENST00000511901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY1R	XM_005263031.5	c.-152+5181C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPY1R	ENST00000511901.1	c.-152+5181C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94504 AN: 151888 Hom.: 31773 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.622 AC: 94504 AN: 152006 Hom.: 31762 Cov.: 31 AF XY: 0.622 AC XY: 46224 AN XY: 74288

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.638

Alfa AF: 0.725 Hom.: 83209

Bravo AF: 0.604

Asia WGS AF: 0.582 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.5
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4234955; hg19: chr4-164260276; COSMIC: COSV58453603;