7-24285390-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_000905.4(NPY):c.150G>A(p.Ser50Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 1,613,318 control chromosomes in the GnomAD database, including 218,988 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.49 ( 18655 hom., cov: 31)

Exomes 𝑓: 0.52 ( 200333 hom. )

Consequence

NPY
NM_000905.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.497

Publications

46 publications found

Variant links:

Genes affected

NPY (HGNC:7955): (neuropeptide Y) This gene encodes a neuropeptide that is widely expressed in the central nervous system and influences many physiological processes, including cortical excitability, stress response, food intake, circadian rhythms, and cardiovascular function. The neuropeptide functions through G protein-coupled receptors to inhibit adenylyl cyclase, activate mitogen-activated protein kinase (MAPK), regulate intracellular calcium levels, and activate potassium channels. A polymorphism in this gene resulting in a change of leucine 7 to proline in the signal peptide is associated with elevated cholesterol levels, higher alcohol consumption, and may be a risk factor for various metabolic and cardiovascular diseases. The protein also exhibits antimicrobial activity against bacteria and fungi. [provided by RefSeq, Oct 2014]

NPY links:

ENSG00000228944 (HGNC:):

ENSG00000228944 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 7-24285390-G-A is Benign according to our data. Variant chr7-24285390-G-A is described in CliVar as Benign. Clinvar id is 1544481.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-24285390-G-A is described in CliVar as Benign. Clinvar id is 1544481.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-24285390-G-A is described in CliVar as Benign. Clinvar id is 1544481.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-24285390-G-A is described in CliVar as Benign. Clinvar id is 1544481.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-24285390-G-A is described in CliVar as Benign. Clinvar id is 1544481.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-24285390-G-A is described in CliVar as Benign. Clinvar id is 1544481.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.497 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY	NM_000905.4 link	c.150G>A	p.Ser50Ser	synonymous_variant	Exon 2 of 4	ENST00000242152.7	NP_000896.1	P01303A4D158

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY	ENST00000242152.7 link	c.150G>A	p.Ser50Ser	synonymous_variant	Exon 2 of 4	1	NM_000905.4	ENSP00000242152.2		P01303

Frequencies

GnomAD3 genomes

AF:

0.487

AC:

73947

AN:

151756

Hom.:

18649

Cov.:

show subpopulations

Gnomad AFR

AF:

0.369

Gnomad AMI

AF:

0.444

Gnomad AMR

AF:

0.605

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.659

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.516

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.510

Gnomad OTH

AF:

0.496

GnomAD2 exomes

AF:

0.541

AC:

134888

AN:

249506

AF XY:

0.534

show subpopulations

Gnomad AFR exome

AF:

0.374

Gnomad AMR exome

AF:

0.710

Gnomad ASJ exome

AF:

0.541

Gnomad EAS exome

AF:

0.653

Gnomad FIN exome

AF:

0.523

Gnomad NFE exome

AF:

0.506

Gnomad OTH exome

AF:

0.528

GnomAD4 exome

AF:

0.521

AC:

761142

AN:

1461444

Hom.:

200333

Cov.:

AF XY:

0.520

AC XY:

377975

AN XY:

726992

show subpopulations

African (AFR)

AF:

0.371

AC:

12407

AN:

33478

American (AMR)

AF:

0.698

AC:

31187

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.548

AC:

14326

AN:

26130

East Asian (EAS)

AF:

0.649

AC:

25754

AN:

39688

South Asian (SAS)

AF:

0.519

AC:

44742

AN:

86244

European-Finnish (FIN)

AF:

0.527

AC:

28043

AN:

53234

Middle Eastern (MID)

AF:

0.477

AC:

2746

AN:

5760

European-Non Finnish (NFE)

AF:

0.513

AC:

570891

AN:

1111826

Other (OTH)

AF:

0.514

AC:

31046

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

20628

41256

61884

82512

103140

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16614

33228

49842

66456

83070

<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:

0.487

AC:

73976

AN:

151874

Hom.:

18655

Cov.:

AF XY:

0.491

AC XY:

36477

AN XY:

74224

show subpopulations

African (AFR)

AF:

0.368

AC:

15249

AN:

41396

American (AMR)

AF:

0.606

AC:

9253

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.539

AC:

1869

AN:

3468

East Asian (EAS)

AF:

0.659

AC:

3381

AN:

5134

South Asian (SAS)

AF:

0.529

AC:

2541

AN:

4804

European-Finnish (FIN)

AF:

0.516

AC:

5442

AN:

10552

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.510

AC:

34643

AN:

67932

Other (OTH)

AF:

0.493

AC:

1040

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1863

3726

5589

7452

9315

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

682

1364

2046

2728

3410

<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:

0.502

Hom.:

16740

Bravo

AF:

0.490

Asia WGS

AF:

0.545

AC:

1895

AN:

3478

EpiCase

AF:

0.502

EpiControl

AF:

0.508

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

5.8

(source)

DANN

Benign

0.95

PhyloP100

-0.50

PromoterAI

-0.0092

Neutral

(source)

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

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over