Menu
GeneBe

7-24289514-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_000905.4(NPY):c.204C>T(p.Ser68=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 1,585,064 control chromosomes in the GnomAD database, including 169,337 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 14177 hom., cov: 30)
Exomes 𝑓: 0.46 ( 155160 hom. )

Consequence

NPY
NM_000905.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.357
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-24289514-C-T is Benign according to our data. Variant chr7-24289514-C-T is described in ClinVar as [Benign]. Clinvar id is 1601323.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=-0.357 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NPYNM_000905.4 linkuse as main transcriptc.204C>T p.Ser68= synonymous_variant 3/4 ENST00000242152.7
LOC107986777XR_001745132.2 linkuse as main transcriptn.209+29843G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NPYENST00000242152.7 linkuse as main transcriptc.204C>T p.Ser68= synonymous_variant 3/41 NM_000905.4 P1
NPYENST00000405982.1 linkuse as main transcriptc.204C>T p.Ser68= synonymous_variant 2/31 P1
NPYENST00000407573.5 linkuse as main transcriptc.204C>T p.Ser68= synonymous_variant 4/53 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.428
AC:
64873
AN:
151484
Hom.:
14178
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.348
Gnomad AMI
AF:
0.441
Gnomad AMR
AF:
0.430
Gnomad ASJ
AF:
0.490
Gnomad EAS
AF:
0.361
Gnomad SAS
AF:
0.344
Gnomad FIN
AF:
0.465
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.478
Gnomad OTH
AF:
0.433
GnomAD3 exomes
AF:
0.429
AC:
100479
AN:
234306
Hom.:
22059
AF XY:
0.426
AC XY:
54021
AN XY:
126910
show subpopulations
Gnomad AFR exome
AF:
0.347
Gnomad AMR exome
AF:
0.436
Gnomad ASJ exome
AF:
0.478
Gnomad EAS exome
AF:
0.345
Gnomad SAS exome
AF:
0.321
Gnomad FIN exome
AF:
0.470
Gnomad NFE exome
AF:
0.466
Gnomad OTH exome
AF:
0.438
GnomAD4 exome
AF:
0.461
AC:
661128
AN:
1433462
Hom.:
155160
Cov.:
32
AF XY:
0.458
AC XY:
326353
AN XY:
712992
show subpopulations
Gnomad4 AFR exome
AF:
0.342
Gnomad4 AMR exome
AF:
0.441
Gnomad4 ASJ exome
AF:
0.487
Gnomad4 EAS exome
AF:
0.320
Gnomad4 SAS exome
AF:
0.332
Gnomad4 FIN exome
AF:
0.470
Gnomad4 NFE exome
AF:
0.480
Gnomad4 OTH exome
AF:
0.444
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.428
AC:
64891
AN:
151602
Hom.:
14177
Cov.:
30
AF XY:
0.425
AC XY:
31457
AN XY:
74056
show subpopulations
Gnomad4 AFR
AF:
0.347
Gnomad4 AMR
AF:
0.431
Gnomad4 ASJ
AF:
0.490
Gnomad4 EAS
AF:
0.359
Gnomad4 SAS
AF:
0.343
Gnomad4 FIN
AF:
0.465
Gnomad4 NFE
AF:
0.478
Gnomad4 OTH
AF:
0.428
Alfa
AF:
0.467
Hom.:
18151
Bravo
AF:
0.424
Asia WGS
AF:
0.296
AC:
1033
AN:
3478

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
-0.40
Cadd
Benign
2.4
Dann
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.14
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: rs5574; hg19: chr7-24329133; COSMIC: COSV54215144; API