Genetic Variant NPY2R-AS1:n.1323T>C (chr4-155206897-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000511017.7(NPY2R-AS1):n.1323T>C 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 0.495 in 151,986 control chromosomes in the GnomAD database, including 20,135 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 ( 20135 hom., cov: 33)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

NPY2R-AS1
ENST00000511017.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.637

Publications

3 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:

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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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2 link	n.1067T>C		non_coding_transcript_exon_variant	Exon 2 of 2
NPY2R	NM_001375470.1 link	c.-48-6995A>G		intron_variant	Intron 1 of 1		NP_001362399.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NPY2R-AS1	ENST00000511017.7 link	n.1323T>C	non_coding_transcript_exon_variant	Exon 3 of 3	3
MAP9-AS1	ENST00000630664.3 link	n.399+32613A>G	intron_variant	Intron 2 of 4	5
NPY2R-AS1	ENST00000727157.1 link	n.361+1128T>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.494

AC:

75062

AN:

151864

Hom.:

20089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.720

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.436

Gnomad ASJ

AF:

0.415

Gnomad EAS

AF:

0.516

Gnomad SAS

AF:

0.366

Gnomad FIN

AF:

0.508

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.383

Gnomad OTH

AF:

0.466

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.495

AC:

75172

AN:

151982

Hom.:

20135

Cov.:

AF XY:

0.494

AC XY:

36733

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.720

AC:

29867

AN:

41482

American (AMR)

AF:

0.436

AC:

6657

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.415

AC:

1436

AN:

3464

East Asian (EAS)

AF:

0.516

AC:

2668

AN:

5170

South Asian (SAS)

AF:

0.365

AC:

1764

AN:

4828

European-Finnish (FIN)

AF:

0.508

AC:

5349

AN:

10530

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.383

AC:

26039

AN:

67934

Other (OTH)

AF:

0.471

AC:

993

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1854

3708

5562

7416

9270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<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:

0.439

Hom.:

2481

Bravo

AF:

0.501

Asia WGS

AF:

0.473

AC:

1644

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.71

(source)

DANN

Benign

0.37

PhyloP100

-0.64

Splicing

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

Publications

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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