chr4-155204358-A-G

Position:

• chr4-155204358-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375470.1(NPY2R):​c.-48-9534A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,008 control chromosomes in the GnomAD database, including 6,979 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 0.29 (6979 hom., cov: 32)
• Consequence: NPY2R NM_001375470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

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]

NPY2R-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPY2R	NM_001375470.1	c.-48-9534A>G		intron_variant			NP_001362399.1
NPY2R-AS1	XR_001741894.2	n.3606T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP9-AS1	ENST00000630664.2	n.208+30074A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44703 AN: 151890 Hom.: 6968 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.294 AC: 44743 AN: 152008 Hom.: 6979 Cov.: 32 AF XY: 0.299 AC XY: 22200 AN XY: 74298

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.288

Alfa AF: 0.292 Hom.: 2222

Bravo AF: 0.284

Asia WGS AF: 0.427 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11099992; hg19: chr4-156125510;