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GeneBe

7-24285390-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_000905.4(NPY):c.150G>A(p.Ser50=) 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

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.497
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-24285390-G-A is Benign according to our data. Variant chr7-24285390-G-A is described in ClinVar as [Benign]. Clinvar id is 1544481.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.497 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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/exons MANE UniProt
NPYNM_000905.4 linkuse as main transcriptc.150G>A p.Ser50= synonymous_variant 2/4 ENST00000242152.7
LOC107986777XR_001745132.2 linkuse as main transcriptn.209+33967C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NPYENST00000242152.7 linkuse as main transcriptc.150G>A p.Ser50= synonymous_variant 2/41 NM_000905.4 P1
NPYENST00000405982.1 linkuse as main transcriptc.150G>A p.Ser50= synonymous_variant 1/31 P1
NPYENST00000407573.5 linkuse as main transcriptc.150G>A p.Ser50= synonymous_variant 3/53 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.487
AC:
73947
AN:
151756
Hom.:
18649
Cov.:
31
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
GnomAD3 exomes
AF:
0.541
AC:
134888
AN:
249506
Hom.:
37635
AF XY:
0.534
AC XY:
72042
AN XY:
134962
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 SAS exome
AF:
0.513
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.:
62
AF XY:
0.520
AC XY:
377975
AN XY:
726992
show subpopulations
Gnomad4 AFR exome
AF:
0.371
Gnomad4 AMR exome
AF:
0.698
Gnomad4 ASJ exome
AF:
0.548
Gnomad4 EAS exome
AF:
0.649
Gnomad4 SAS exome
AF:
0.519
Gnomad4 FIN exome
AF:
0.527
Gnomad4 NFE exome
AF:
0.513
Gnomad4 OTH exome
AF:
0.514
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.487
AC:
73976
AN:
151874
Hom.:
18655
Cov.:
31
AF XY:
0.491
AC XY:
36477
AN XY:
74224
show subpopulations
Gnomad4 AFR
AF:
0.368
Gnomad4 AMR
AF:
0.606
Gnomad4 ASJ
AF:
0.539
Gnomad4 EAS
AF:
0.659
Gnomad4 SAS
AF:
0.529
Gnomad4 FIN
AF:
0.516
Gnomad4 NFE
AF:
0.510
Gnomad4 OTH
AF:
0.493
Alfa
AF:
0.503
Hom.:
12114
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
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
5.8
Dann
Benign
0.95

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5573; hg19: chr7-24325009; COSMIC: COSV54215135; API