4-155206115-T-C

Variant names:

• chr4-155206115-T-C
• rs10212868
• XR_001741894.2:n.1849A>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.1849A>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 0.496 in 151,952 control chromosomes in the GnomAD database, including 20,245 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 0.50 (20245 hom., cov: 32)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2	n.1849A>G		non_coding_transcript_exon_variant	Exon 2 of 2
NPY2R	NM_001375470.1	c.-48-7777T>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+31831T>C		intron_variant	Intron 2 of 4	5
NPY2R-AS1	ENST00000727157.1	n.361+1910A>G		intron_variant	Intron 2 of 4
NPY2R-AS1	ENST00000727158.1	n.292+1910A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75295 AN: 151834 Hom.: 20199 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.496 AC: 75405 AN: 151952 Hom.: 20245 Cov.: 32 AF XY: 0.496 AC XY: 36823 AN XY: 74242

African (AFR) AF: 0.721 AC: 29863 AN: 41446

American (AMR) AF: 0.436 AC: 6657 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1438 AN: 3472

East Asian (EAS) AF: 0.516 AC: 2649 AN: 5138

South Asian (SAS) AF: 0.366 AC: 1763 AN: 4822

European-Finnish (FIN) AF: 0.510 AC: 5380 AN: 10540

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26261 AN: 67962

Other (OTH) AF: 0.473 AC: 995 AN: 2104

Alfa AF: 0.424 Hom.: 6707

Bravo AF: 0.502

Asia WGS AF: 0.473 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.27
DANN	Benign	0.65
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10212868; hg19: chr4-156127267; COSMIC: COSV107344646;