dbSNP rs9764: NPY1R:c.*1050A>G (chr4-163324253-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000909.6(NPY1R):c.*1050A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,466 control chromosomes in the GnomAD database, including 7,509 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 0.30 ( 7458 hom., cov: 32)

Exomes 𝑓: 0.43 ( 51 hom. )

Consequence

NPY1R
NM_000909.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39

Publications

22 publications found

Variant links:

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]

NPY1R links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
NPY1R	NM_000909.6 link	c.*1050A>G	3_prime_UTR_variant	Exon 3 of 3	ENST00000296533.3	NP_000900.1	P25929
NPY1R	XM_005263031.5 link	c.*1050A>G	3_prime_UTR_variant	Exon 3 of 3		XP_005263088.1	P25929
NPY1R	XM_011532010.4 link	c.*1050A>G	3_prime_UTR_variant	Exon 3 of 3		XP_011530312.1	P25929

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY1R	ENST00000296533.3 link	c.*1050A>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_000909.6	ENSP00000354652.2		P25929

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46194

AN:

151916

Hom.:

7449

Cov.:

show subpopulations

Gnomad AFR

AF:

0.333

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.562

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.278

GnomAD4 exome

AF:

0.428

AC:

185

AN:

432

Hom.:

Cov.:

AF XY:

0.423

AC XY:

110

AN XY:

260

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.425

AC:

181

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.304

AC:

46232

AN:

152034

Hom.:

7458

Cov.:

AF XY:

0.307

AC XY:

22852

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.333

AC:

13831

AN:

41484

American (AMR)

AF:

0.232

AC:

3551

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

889

AN:

3466

East Asian (EAS)

AF:

0.561

AC:

2903

AN:

5172

South Asian (SAS)

AF:

0.268

AC:

1291

AN:

4824

European-Finnish (FIN)

AF:

0.434

AC:

4582

AN:

10546

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.271

AC:

18409

AN:

67946

Other (OTH)

AF:

0.274

AC:

579

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1650

3299

4949

6598

8248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

476

952

1428

1904

2380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.271

Hom.:

7981

Bravo

AF:

0.296

Asia WGS

AF:

0.348

AC:

1211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.0

(source)

DANN

Benign

0.62

PhyloP100

1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over