Variant chr7-24289484-C-CT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000905.4(NPY):c.189-5dup variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,327,044 control chromosomes in the GnomAD database, including 6,782 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1112 hom., cov: 30)

Exomes 𝑓: 0.16 ( 5670 hom. )

Consequence

NPY
NM_000905.4 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.00900

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 -10 ACMG points.

BP6

Variant 7-24289484-C-CT is Benign according to our data. Variant chr7-24289484-C-CT is described in ClinVar as [Benign]. Clinvar id is 1665605.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPY	NM_000905.4 linkuse as main transcript	c.189-5dup		splice_polypyrimidine_tract_variant, intron_variant		ENST00000242152.7
LOC107986777	XR_001745132.2 linkuse as main transcript	n.209+29872_209+29873insA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
NPY	ENST00000242152.7 linkuse as main transcript	c.189-5dup	splice_polypyrimidine_tract_variant, intron_variant	1	NM_000905.4	P1
NPY	ENST00000405982.1 linkuse as main transcript	c.189-5dup	splice_polypyrimidine_tract_variant, intron_variant	1		P1
NPY	ENST00000407573.5 linkuse as main transcript	c.189-5dup	splice_polypyrimidine_tract_variant, intron_variant	3		P1

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

17885

AN:

150260

Hom.:

1112

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0876

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.0594

Gnomad SAS

AF:

0.0776

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.120

GnomAD3 exomes

AF:

0.158

AC:

25810

AN:

162948

Hom.:

533

AF XY:

0.160

AC XY:

14130

AN XY:

88446

show subpopulations

Gnomad AFR exome

AF:

0.121

Gnomad AMR exome

AF:

0.106

Gnomad ASJ exome

AF:

0.198

Gnomad EAS exome

AF:

0.101

Gnomad SAS exome

AF:

0.130

Gnomad FIN exome

AF:

0.169

Gnomad NFE exome

AF:

0.183

Gnomad OTH exome

AF:

0.185

GnomAD4 exome

AF:

0.164

AC:

192445

AN:

1176676

Hom.:

5670

Cov.:

AF XY:

0.162

AC XY:

95080

AN XY:

585584

show subpopulations

Gnomad4 AFR exome

AF:

0.102

Gnomad4 AMR exome

AF:

0.0845

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.0662

Gnomad4 SAS exome

AF:

0.110

Gnomad4 FIN exome

AF:

0.141

Gnomad4 NFE exome

AF:

0.177

Gnomad4 OTH exome

AF:

0.161

GnomAD4 genome

AF:

0.119

AC:

17882

AN:

150368

Hom.:

1112

Cov.:

AF XY:

0.117

AC XY:

8547

AN XY:

73332

show subpopulations

Gnomad4 AFR

AF:

0.0874

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.158

Gnomad4 EAS

AF:

0.0593

Gnomad4 SAS

AF:

0.0778

Gnomad4 FIN

AF:

0.116

Gnomad4 NFE

AF:

0.147

Gnomad4 OTH

AF:

0.118

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

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