7-24291197-G-A

Variant names:

• chr7-24291197-G-A
• rs4722343
• NM_000905.4:c.270-466G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000905.4(NPY):​c.270-466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 152,260 control chromosomes in the GnomAD database, including 71,682 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.97 (71682 hom., cov: 30)
• Consequence: NPY NM_000905.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 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.270-466G>A		intron	N/A	NP_000896.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY	ENST00000242152.7	TSL:1 MANE Select	c.270-466G>A		intron	N/A	ENSP00000242152.2
	NPY	ENST00000405982.1	TSL:1	c.270-466G>A		intron	N/A	ENSP00000385282.1
	NPY	ENST00000407573.5	TSL:3	c.270-466G>A		intron	N/A	ENSP00000384364.1

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147610 AN: 152142 Hom.: 71630 Cov.: 30

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.973

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.970 AC: 147720 AN: 152260 Hom.: 71682 Cov.: 30 AF XY: 0.971 AC XY: 72301 AN XY: 74444

African (AFR) AF: 0.993 AC: 41233 AN: 41538

American (AMR) AF: 0.976 AC: 14927 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3365 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5181 AN: 5184

South Asian (SAS) AF: 0.987 AC: 4758 AN: 4820

European-Finnish (FIN) AF: 0.948 AC: 10054 AN: 10602

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64974 AN: 68028

Other (OTH) AF: 0.969 AC: 2046 AN: 2112

Alfa AF: 0.961 Hom.: 8723

Bravo AF: 0.974

Asia WGS AF: 0.985 AC: 3424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.47
PhyloP100		1.3
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: rs4722343; hg19: chr7-24330816;