rs2880414

Variant names:

• chr4-155172499-A-C
• rs2880414
• ENST00000727157.1:n.464+18226T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-155172499-A-C
• chr4-155172499-A-T

Variant summary

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

The ENST00000727157.1(NPY2R-AS1):​n.464+18226T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,530 control chromosomes in the GnomAD database, including 14,740 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 0.41 (14740 hom., cov: 30)
• Consequence: NPY2R-AS1 ENST00000727157.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 6 publications found

Genes affected

NPY2R-AS1 (HGNC:55549): (NPY2R antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPY2R-AS1	ENST00000727157.1	n.464+18226T>G		intron_variant	Intron 3 of 4
NPY2R-AS1	ENST00000727158.1	n.395+18226T>G		intron_variant	Intron 3 of 4
NPY2R-AS1	ENST00000727159.1	n.444-3334T>G		intron_variant	Intron 3 of 4
NPY2R-AS1	ENST00000727160.1	n.497-3334T>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61488 AN: 151410 Hom.: 14709 Cov.: 30

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.406 AC: 61566 AN: 151530 Hom.: 14740 Cov.: 30 AF XY: 0.412 AC XY: 30500 AN XY: 73970

African (AFR) AF: 0.665 AC: 27472 AN: 41314

American (AMR) AF: 0.392 AC: 5960 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3466

East Asian (EAS) AF: 0.430 AC: 2203 AN: 5122

South Asian (SAS) AF: 0.393 AC: 1886 AN: 4802

European-Finnish (FIN) AF: 0.357 AC: 3737 AN: 10464

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18420 AN: 67854

Other (OTH) AF: 0.387 AC: 815 AN: 2104

Alfa AF: 0.307 Hom.: 34380

Bravo AF: 0.416

Asia WGS AF: 0.425 AC: 1477 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.72
DANN	Benign	0.45
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2880414; hg19: chr4-156093651;