rs2342676

Variant names:

• chr4-155203552-T-C
• rs2342676
• XR_001741894.2:n.4412A>G

Variant summary

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

The XR_001741894.2(NPY2R-AS1):​n.4412A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,748 control chromosomes in the GnomAD database, including 17,981 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 (17981 hom., cov: 32)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2	n.4412A>G		non_coding_transcript_exon_variant	Exon 2 of 2
NPY2R	NM_001375470.1	c.-48-10340T>C		intron_variant	Intron 1 of 1		NP_001362399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP9-AS1	ENST00000630664.3	n.399+29268T>C		intron_variant	Intron 2 of 4	5
NPY2R-AS1	ENST00000727157.1	n.361+4473A>G		intron_variant	Intron 2 of 4
NPY2R-AS1	ENST00000727158.1	n.292+4473A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71784 AN: 151632 Hom.: 17943 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.474 AC: 71886 AN: 151748 Hom.: 17981 Cov.: 32 AF XY: 0.475 AC XY: 35186 AN XY: 74150

African (AFR) AF: 0.644 AC: 26672 AN: 41432

American (AMR) AF: 0.428 AC: 6520 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2625 AN: 5112

South Asian (SAS) AF: 0.365 AC: 1761 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5450 AN: 10522

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26070 AN: 67850

Other (OTH) AF: 0.458 AC: 965 AN: 2106

Alfa AF: 0.428 Hom.: 1846

Bravo AF: 0.477

Asia WGS AF: 0.470 AC: 1636 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.83
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs2342676; hg19: chr4-156124704;