rs5573

Variant names:

• chr7-24285390-G-A
• rs5573
• NM_000905.4:c.150G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-24285390-G-A
• chr7-24285390-G-C
• chr7-24285390-G-T

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.497
• Publications: 46 publications found

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]

ENSG00000228944 (HGNC:):

ACMG classification

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 ClinVar as Benign. ClinVar VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000905.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY	NM_000905.4	MANE Select	c.150G>A	p.Ser50Ser	synonymous	Exon 2 of 4	NP_000896.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY	ENST00000242152.7	TSL:1 MANE Select	c.150G>A	p.Ser50Ser	synonymous	Exon 2 of 4	ENSP00000242152.2
	NPY	ENST00000405982.1	TSL:1	c.150G>A	p.Ser50Ser	synonymous	Exon 1 of 3	ENSP00000385282.1
	NPY	ENST00000407573.5	TSL:3	c.150G>A	p.Ser50Ser	synonymous	Exon 3 of 5	ENSP00000384364.1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73947 AN: 151756 Hom.: 18649 Cov.: 31

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

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.: 62 AF XY: 0.520 AC XY: 377975 AN XY: 726992

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

GnomAD4 genome AF: 0.487 AC: 73976 AN: 151874 Hom.: 18655 Cov.: 31 AF XY: 0.491 AC XY: 36477 AN XY: 74224

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

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	5.8
DANN	Benign	0.95
PhyloP100		-0.50
PromoterAI		-0.0092	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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