rs12641982

Variant names:

• chr4-155202442-A-G
• rs12641982
• XR_001741894.2:n.5522T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-155202442-A-G
• chr4-155202442-A-T

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.5522T>C 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 0.714 in 152,074 control chromosomes in the GnomAD database, including 40,339 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 0.71 (40339 hom., cov: 32)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2	n.5522T>C		non_coding_transcript_exon_variant	Exon 2 of 2
NPY2R	NM_001375470.1	c.-48-11450A>G		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+28158A>G		intron_variant	Intron 2 of 4	5
NPY2R-AS1	ENST00000727157.1	n.361+5583T>C		intron_variant	Intron 2 of 4
NPY2R-AS1	ENST00000727158.1	n.292+5583T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108403 AN: 151956 Hom.: 40290 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.714 AC: 108514 AN: 152074 Hom.: 40339 Cov.: 32 AF XY: 0.725 AC XY: 53946 AN XY: 74368

African (AFR) AF: 0.886 AC: 36772 AN: 41498

American (AMR) AF: 0.721 AC: 11016 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1898 AN: 3468

East Asian (EAS) AF: 0.941 AC: 4861 AN: 5168

South Asian (SAS) AF: 0.770 AC: 3716 AN: 4828

European-Finnish (FIN) AF: 0.788 AC: 8351 AN: 10598

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39841 AN: 67914

Other (OTH) AF: 0.691 AC: 1462 AN: 2116

Alfa AF: 0.683 Hom.: 5201

Bravo AF: 0.711

Asia WGS AF: 0.867 AC: 3016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.56
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs12641982; hg19: chr4-156123594;