Genetic Variant NPY5R:c.*433G>A (chr4-163352044-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XM_005263038.4(NPY5R):c.*433G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 156,200 control chromosomes in the GnomAD database, including 553 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 0.079 ( 539 hom., cov: 33)

Exomes 𝑓: 0.084 ( 14 hom. )

Consequence

NPY5R
XM_005263038.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Publications

1 publications found

Variant links:

Genes affected

NPY5R (HGNC:7958): (neuropeptide Y receptor Y5) The protein encoded by this gene is a receptor for neuropeptide Y and peptide YY. The encoded protein appears to be involved in regulating food intake, with defects in this gene being associated with eating disorders. Also, the encoded protein is involved in a pathway that protects neuroblastoma cells from chemotherapy-induced cell death, providing a possible therapeutic target against neuroblastoma. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Nov 2015]

NPY5R 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000338566.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NPY5R	NM_006174.4	MANE Select	c.*433G>A	downstream_gene	N/A	NP_006165.1
NPY5R	NM_001317091.2		c.*433G>A	downstream_gene	N/A	NP_001304020.1
NPY5R	NM_001317092.2		c.*433G>A	downstream_gene	N/A	NP_001304021.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY5R	ENST00000338566.8	TSL:1 MANE Select	c.*433G>A		downstream_gene	N/A	ENSP00000339377.3
	NPY5R	ENST00000515560.1	TSL:2	c.*433G>A		downstream_gene	N/A	ENSP00000423917.1

Frequencies

GnomAD3 genomes

AF:

0.0795

AC:

12082

AN:

151930

Hom.:

543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0773

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0947

Gnomad ASJ

AF:

0.0664

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.0821

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0668

Gnomad OTH

AF:

0.0755

GnomAD4 exome

AF:

0.0838

AC:

348

AN:

4152

Hom.:

AF XY:

0.0817

AC XY:

175

AN XY:

2142

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.100

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.0625

AC:

AN:

East Asian (EAS)

AF:

0.0625

AC:

AN:

South Asian (SAS)

AF:

0.286

AC:

AN:

European-Finnish (FIN)

AF:

0.0881

AC:

324

AN:

3676

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0357

AC:

AN:

364

Other (OTH)

AF:

0.0500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0794

AC:

12075

AN:

152048

Hom.:

539

Cov.:

AF XY:

0.0814

AC XY:

6046

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.0772

AC:

3204

AN:

41508

American (AMR)

AF:

0.0948

AC:

1448

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0664

AC:

230

AN:

3466

East Asian (EAS)

AF:

0.141

AC:

729

AN:

5182

South Asian (SAS)

AF:

0.177

AC:

852

AN:

4816

European-Finnish (FIN)

AF:

0.0821

AC:

866

AN:

10544

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0669

AC:

4543

AN:

67942

Other (OTH)

AF:

0.0747

AC:

158

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

563

1125

1688

2250

2813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<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:

0.0358

Hom.:

Bravo

AF:

0.0817

Asia WGS

AF:

0.148

AC:

513

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.35

(source)

DANN

Benign

0.44

PhyloP100

-1.3

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over