rs1902491

Variant names:

• chr4-155134181-C-A
• rs1902491
• ENST00000727157.1:n.564+1341G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-155134181-C-A
• chr4-155134181-C-G
• chr4-155134181-C-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.564+1341G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,852 control chromosomes in the GnomAD database, including 14,539 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 0.43 (14539 hom., cov: 32)
• Consequence: NPY2R-AS1 ENST00000727157.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727157.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPY2R-AS1	ENST00000727157.1		n.564+1341G>T		intron	N/A
	NPY2R-AS1	ENST00000727158.1		n.495+1341G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64709 AN: 151734 Hom.: 14527 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.426 AC: 64764 AN: 151852 Hom.: 14539 Cov.: 32 AF XY: 0.439 AC XY: 32549 AN XY: 74150

African (AFR) AF: 0.381 AC: 15749 AN: 41384

American (AMR) AF: 0.471 AC: 7185 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3470

East Asian (EAS) AF: 0.825 AC: 4244 AN: 5142

South Asian (SAS) AF: 0.543 AC: 2611 AN: 4812

European-Finnish (FIN) AF: 0.555 AC: 5836 AN: 10524

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26437 AN: 67952

Other (OTH) AF: 0.430 AC: 908 AN: 2110

Alfa AF: 0.383 Hom.: 7080

Bravo AF: 0.416

Asia WGS AF: 0.673 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.63
DANN	Benign	0.60
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1902491; hg19: chr4-156055333;