rs33977152

Variant names:

• chr4-155207437-G-A
• rs33977152
• ENST00000508687.2:n.722C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-155207437-G-A
• chr4-155207437-G-C

Variant summary

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

The ENST00000508687.2(NPY2R-AS1):​n.722C>T 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 0.26 in 152,158 control chromosomes in the GnomAD database, including 6,159 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 (6159 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NPY2R-AS1 ENST00000508687.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2	n.527C>T		non_coding_transcript_exon_variant	Exon 2 of 2
NPY2R	NM_001375470.1	c.-48-6455G>A		intron_variant	Intron 1 of 1		NP_001362399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY2R-AS1	ENST00000508687.2	n.722C>T		non_coding_transcript_exon_variant	Exon 3 of 3	3
NPY2R-AS1	ENST00000511017.7	n.783C>T		non_coding_transcript_exon_variant	Exon 3 of 3	3
NPY2R-AS1	ENST00000727161.1	n.864C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39596 AN: 152040 Hom.: 6148 Cov.: 33

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.258

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.260 AC: 39620 AN: 152158 Hom.: 6159 Cov.: 33 AF XY: 0.267 AC XY: 19835 AN XY: 74390

African (AFR) AF: 0.0994 AC: 4129 AN: 41554

American (AMR) AF: 0.300 AC: 4578 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1115 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2654 AN: 5166

South Asian (SAS) AF: 0.348 AC: 1678 AN: 4816

European-Finnish (FIN) AF: 0.410 AC: 4337 AN: 10580

Middle Eastern (MID) AF: 0.252 AC: 73 AN: 290

European-Non Finnish (NFE) AF: 0.299 AC: 20311 AN: 67976

Other (OTH) AF: 0.265 AC: 559 AN: 2112

Alfa AF: 0.289 Hom.: 1937

Bravo AF: 0.245

Asia WGS AF: 0.421 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.87
DANN	Benign	0.76
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs33977152; hg19: chr4-156128589;