4-155190827-A-C

Variant names:

• chr4-155190827-A-C
• rs2880412
• ENST00000727157.1:n.362T>G

Variant summary

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

The ENST00000727157.1(NPY2R-AS1):​n.362T>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,776 control chromosomes in the GnomAD database, including 5,716 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 0.26 (5716 hom., cov: 32)
• Consequence: NPY2R-AS1 ENST00000727157.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 1 publications found

Genes affected

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

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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727157.1. 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+17031A>C		intron	N/A	NP_001362399.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY2R-AS1	ENST00000727157.1		n.362T>G		splice_region non_coding_transcript_exon	Exon 3 of 5
	NPY2R-AS1	ENST00000727158.1		n.293T>G		splice_region non_coding_transcript_exon	Exon 3 of 5
	NPY2R-AS1	ENST00000727159.1		n.341T>G		splice_region non_coding_transcript_exon	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38720 AN: 151658 Hom.: 5700 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.255 AC: 38766 AN: 151776 Hom.: 5716 Cov.: 32 AF XY: 0.261 AC XY: 19390 AN XY: 74180

African (AFR) AF: 0.126 AC: 5237 AN: 41490

American (AMR) AF: 0.290 AC: 4416 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 954 AN: 3458

East Asian (EAS) AF: 0.531 AC: 2734 AN: 5148

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4814

European-Finnish (FIN) AF: 0.392 AC: 4129 AN: 10536

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18972 AN: 67800

Other (OTH) AF: 0.255 AC: 538 AN: 2108

Alfa AF: 0.262 Hom.: 690

Bravo AF: 0.242

Asia WGS AF: 0.423 AC: 1468 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2880412; hg19: chr4-156111979;