rs13306006

chr4-163332563-C-T

Variant summary

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

The NM_000909.6(NPY1R):c.-233G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 152,218 control chromosomes in the GnomAD database, including 97 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 0.021 (97 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NPY1R NM_000909.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

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=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY1R	NM_000909.6	c.-233G>A		5_prime_UTR_variant	1/3	ENST00000296533.3
NPY1R	XM_011532010.4	c.-2015G>A		5_prime_UTR_variant	1/3
NPY1R	XM_005263031.5	c.-151-5858G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPY1R	ENST00000296533.3	c.-233G>A		5_prime_UTR_variant	1/3	1	NM_000909.6	P1

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3267 AN: 152100 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00456

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.0540

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0244

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 50 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 26

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0215 AC: 3272 AN: 152218 Hom.: 97 Cov.: 32 AF XY: 0.0231 AC XY: 1721 AN XY: 74416

Gnomad4 AFR AF: 0.00453

Gnomad4 AMR AF: 0.0744

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.0329

Gnomad4 SAS AF: 0.0534

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.0184

Gnomad4 OTH AF: 0.0266

Alfa AF: 0.0213 Hom.: 23

Bravo AF: 0.0233

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	5.3
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13306006; hg19: chr4-164253715;