NM_001375470.1:c.-49+17905T>G

Variant names:

• chr4-155191701-T-G
• rs10517606
• NM_001375470.1:c.-49+17905T>G

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+17905T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,642 control chromosomes in the GnomAD database, including 13,773 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 0.42 (13773 hom., cov: 32)
• Consequence: NPY2R NM_001375470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY2R	NM_001375470.1		c.-49+17905T>G		intron	N/A	NP_001362399.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP9-AS1	ENST00000630664.3	TSL:5	n.399+17417T>G		intron	N/A
	NPY2R-AS1	ENST00000727157.1		n.362-874A>C		intron	N/A
	NPY2R-AS1	ENST00000727158.1		n.293-874A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63497 AN: 151524 Hom.: 13751 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.419 AC: 63564 AN: 151642 Hom.: 13773 Cov.: 32 AF XY: 0.426 AC XY: 31559 AN XY: 74104

African (AFR) AF: 0.399 AC: 16510 AN: 41414

American (AMR) AF: 0.448 AC: 6808 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1296 AN: 3452

East Asian (EAS) AF: 0.693 AC: 3567 AN: 5144

South Asian (SAS) AF: 0.468 AC: 2256 AN: 4816

European-Finnish (FIN) AF: 0.521 AC: 5505 AN: 10560

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26390 AN: 67752

Other (OTH) AF: 0.392 AC: 826 AN: 2108

Alfa AF: 0.398 Hom.: 32985

Bravo AF: 0.411

Asia WGS AF: 0.577 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.61
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10517606; hg19: chr4-156112853;