chr4-163339124-G-A

Variant names:

• chr4-163339124-G-A
• rs4234955
• ENST00000511901.1:c.-152+5181C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511901.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY1R	ENST00000511901.1	TSL:3	c.-152+5181C>T		intron	N/A	ENSP00000423878.1

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

African (AFR) AF: 0.350 AC: 14486 AN: 41446

American (AMR) AF: 0.668 AC: 10196 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2314 AN: 3468

East Asian (EAS) AF: 0.636 AC: 3281 AN: 5156

South Asian (SAS) AF: 0.573 AC: 2755 AN: 4808

European-Finnish (FIN) AF: 0.768 AC: 8126 AN: 10580

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51124 AN: 67958

Other (OTH) AF: 0.638 AC: 1349 AN: 2116

Alfa AF: 0.707 Hom.: 174738

Bravo AF: 0.604

Asia WGS AF: 0.582 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.43
PhyloP100		0.051

Splicing

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

Other links and lift over

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