rs13306006

Variant names:

• chr4-163332563-C-T
• rs13306006
• NM_000909.6:c.-233G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000909.6. 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
	NPY1R	NM_000909.6	MANE Select	c.-233G>A		5_prime_UTR	Exon 1 of 3	NP_000900.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY1R	ENST00000296533.3	TSL:1 MANE Select	c.-233G>A		5_prime_UTR	Exon 1 of 3	ENSP00000354652.2
	NPY1R	ENST00000509586.5	TSL:2	c.-229G>A		5_prime_UTR	Exon 1 of 4	ENSP00000427284.1
	NPY1R	ENST00000512819.1	TSL:4	c.-237G>A		5_prime_UTR	Exon 1 of 4	ENSP00000421618.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 34

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.00453 AC: 188 AN: 41534

American (AMR) AF: 0.0744 AC: 1137 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3470

East Asian (EAS) AF: 0.0329 AC: 170 AN: 5166

South Asian (SAS) AF: 0.0534 AC: 257 AN: 4814

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0184 AC: 1249 AN: 68028

Other (OTH) AF: 0.0266 AC: 56 AN: 2108

Alfa AF: 0.0214 Hom.: 29

Bravo AF: 0.0233

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		-0.45
PromoterAI		-0.081	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13306006; hg19: chr4-164253715;