Genetic Variant NPY2R-AS1:n.338G>A (chr4-155208030-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000508687.2(NPY2R-AS1):n.338G>A 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 0.493 in 152,184 control chromosomes in the GnomAD database, including 20,038 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 0.49 ( 20027 hom., cov: 32)

Exomes 𝑓: 0.35 ( 11 hom. )

Consequence

NPY2R-AS1
ENST00000508687.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.69

Publications

17 publications found

Variant links:

Genes affected

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

NPY2R-AS1 links:

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]

NPY2R links:

MAP9-AS1 (HGNC:56110): (MAP9 antisense RNA 1)

MAP9-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2 link	n.143G>A		non_coding_transcript_exon_variant	Exon 1 of 2
NPY2R	NM_001375470.1 link	c.-48-5862C>T		intron_variant	Intron 1 of 1		NP_001362399.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NPY2R-AS1	ENST00000508687.2 link	n.338G>A	non_coding_transcript_exon_variant	Exon 2 of 3	3
NPY2R-AS1	ENST00000511017.7 link	n.399G>A	non_coding_transcript_exon_variant	Exon 2 of 3	3
NPY2R-AS1	ENST00000727157.1 link	n.356G>A	non_coding_transcript_exon_variant	Exon 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.493

AC:

74811

AN:

151898

Hom.:

19981

Cov.:

show subpopulations

Gnomad AFR

AF:

0.717

Gnomad AMI

AF:

0.267

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.516

Gnomad SAS

AF:

0.366

Gnomad FIN

AF:

0.509

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.382

Gnomad OTH

AF:

0.463

GnomAD4 exome

AF:

0.351

AC:

AN:

168

Hom.:

Cov.:

AF XY:

0.344

AC XY:

AN XY:

128

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.356

AC:

AN:

132

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.493

AC:

74921

AN:

152016

Hom.:

20027

Cov.:

AF XY:

0.493

AC XY:

36652

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.718

AC:

29782

AN:

41492

American (AMR)

AF:

0.431

AC:

6587

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

1420

AN:

3472

East Asian (EAS)

AF:

0.516

AC:

2643

AN:

5124

South Asian (SAS)

AF:

0.365

AC:

1756

AN:

4814

European-Finnish (FIN)

AF:

0.509

AC:

5389

AN:

10580

Middle Eastern (MID)

AF:

0.521

AC:

152

AN:

292

European-Non Finnish (NFE)

AF:

0.382

AC:

25965

AN:

67962

Other (OTH)

AF:

0.468

AC:

985

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1808

3616

5423

7231

9039

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

644

1288

1932

2576

3220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.394

Hom.:

9533

Bravo

AF:

0.497

Asia WGS

AF:

0.472

AC:

1644

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.39

(source)

DANN

Benign

0.76

PhyloP100

-4.7

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over