4-155186084-C-T

Variant names:

• chr4-155186084-C-T
• rs4425326
• NM_001375470.1:c.-49+12288C>T

Variant summary

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

The NM_001375470.1(NPY2R):​c.-49+12288C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,870 control chromosomes in the GnomAD database, including 17,347 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 0.47 (17347 hom., cov: 32)
• Consequence: NPY2R NM_001375470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 8 publications found

Genes affected

NPY2R (HGNC:7957): (neuropeptide Y receptor Y2) Predicted to enable calcium channel regulator activity and neuropeptide Y receptor activity. Involved in cardiac left ventricle morphogenesis and outflow tract morphogenesis. Located in cilium. Implicated in Huntington's disease; morbid obesity; and obesity. Biomarker of peripheral artery disease and temporal lobe epilepsy. [provided by Alliance of Genome Resources, Apr 2022]

MAP9-AS1 (HGNC:56110): (MAP9 antisense RNA 1)

NPY2R-AS1 (HGNC:55549): (NPY2R antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375470.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY2R	NM_001375470.1		c.-49+12288C>T		intron	N/A	NP_001362399.1	P49146

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP9-AS1	ENST00000630664.3	TSL:5	n.399+11800C>T		intron	N/A
	NPY2R-AS1	ENST00000727157.1		n.464+4641G>A		intron	N/A
	NPY2R-AS1	ENST00000727158.1		n.395+4641G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71007 AN: 151750 Hom.: 17316 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.468 AC: 71094 AN: 151870 Hom.: 17347 Cov.: 32 AF XY: 0.473 AC XY: 35131 AN XY: 74218

African (AFR) AF: 0.565 AC: 23410 AN: 41448

American (AMR) AF: 0.469 AC: 7157 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3468

East Asian (EAS) AF: 0.694 AC: 3575 AN: 5148

South Asian (SAS) AF: 0.472 AC: 2271 AN: 4816

European-Finnish (FIN) AF: 0.522 AC: 5491 AN: 10516

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.391 AC: 26544 AN: 67910

Other (OTH) AF: 0.431 AC: 910 AN: 2112

Alfa AF: 0.416 Hom.: 7038

Bravo AF: 0.466

Asia WGS AF: 0.589 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.45
PhyloP100		-0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4425326; hg19: chr4-156107236;