Variant 7-24285390-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000242152.7(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
ENST00000242152.7 synonymous

Scores

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]

NPY links:

LOC107986777 (HGNC:):

LOC107986777 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 ClinVar 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/exons	MANE	Protein	UniProt
NPY	NM_000905.4 linkuse as main transcript	c.150G>A	p.Ser50=	synonymous_variant	2/4	ENST00000242152.7	NP_000896.1
LOC107986777	XR_001745132.2 linkuse as main transcript	n.209+33967C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
NPY	ENST00000242152.7 linkuse as main transcript	c.150G>A	p.Ser50=	synonymous_variant	2/4	1	NM_000905.4	ENSP00000242152	P1
NPY	ENST00000405982.1 linkuse as main transcript	c.150G>A	p.Ser50=	synonymous_variant	1/3	1		ENSP00000385282	P1
NPY	ENST00000407573.5 linkuse as main transcript	c.150G>A	p.Ser50=	synonymous_variant	3/5	3		ENSP00000384364	P1

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

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.:

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

AF:

0.487

AC:

73976

AN:

151874

Hom.:

18655

Cov.:

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over