rs6849115

Variant names:

• chr4-155203071-T-C
• rs6849115
• XR_001741894.2:n.4893A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001741894.2(NPY2R-AS1):​n.4893A>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 0.238 in 152,018 control chromosomes in the GnomAD database, including 4,645 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 0.24 (4645 hom., cov: 33)
• Consequence: NPY2R-AS1 XR_001741894.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 6 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2	n.4893A>G		non_coding_transcript_exon_variant	Exon 2 of 2
NPY2R	NM_001375470.1	c.-48-10821T>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+28787T>C		intron_variant	Intron 2 of 4	5
NPY2R-AS1	ENST00000727157.1	n.361+4954A>G		intron_variant	Intron 2 of 4
NPY2R-AS1	ENST00000727158.1	n.292+4954A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36141 AN: 151900 Hom.: 4647 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.238 AC: 36140 AN: 152018 Hom.: 4645 Cov.: 33 AF XY: 0.248 AC XY: 18454 AN XY: 74296

African (AFR) AF: 0.239 AC: 9902 AN: 41502

American (AMR) AF: 0.292 AC: 4454 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3466

East Asian (EAS) AF: 0.424 AC: 2189 AN: 5168

South Asian (SAS) AF: 0.404 AC: 1946 AN: 4820

European-Finnish (FIN) AF: 0.268 AC: 2826 AN: 10564

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13671 AN: 67926

Other (OTH) AF: 0.232 AC: 488 AN: 2106

Alfa AF: 0.210 Hom.: 8345

Bravo AF: 0.233

Asia WGS AF: 0.393 AC: 1361 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	16
DANN	Benign	0.75
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs6849115; hg19: chr4-156124223;