Variant rs33977152 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001375470.1(NPY2R):c.-48-6455G>A variant causes a intron 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
NM_001375470.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.626

Variant links:

Genes affected

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:

NPY2R-AS1 (HGNC:):

NPY2R-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NPY2R	NM_001375470.1 linkuse as main transcript	c.-48-6455G>A		intron_variant			NP_001362399.1
NPY2R-AS1	XR_001741894.2 linkuse as main transcript	n.527C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
NPY2R-AS1	ENST00000508687.1 linkuse as main transcript	n.597C>T	non_coding_transcript_exon_variant	3/3	3
NPY2R-AS1	ENST00000511017.6 linkuse as main transcript	n.707C>T	non_coding_transcript_exon_variant	3/3	3
MAP9-AS1	ENST00000630664.2 linkuse as main transcript	n.208+33153G>A	intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39596

AN:

152040

Hom.:

6148

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.260

AC:

39620

AN:

152158

Hom.:

6159

Cov.:

AF XY:

0.267

AC XY:

19835

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0994

Gnomad4 AMR

AF:

0.300

Gnomad4 ASJ

AF:

0.321

Gnomad4 EAS

AF:

0.514

Gnomad4 SAS

AF:

0.348

Gnomad4 FIN

AF:

0.410

Gnomad4 NFE

AF:

0.299

Gnomad4 OTH

AF:

0.265

Alfa

AF:

0.266

Hom.:

726

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over