Variant rs12507396 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000511017.6(NPY2R-AS1):n.329-77T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,222 control chromosomes in the GnomAD database, including 983 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 0.10 ( 982 hom., cov: 33)

Exomes 𝑓: 0.16 ( 1 hom. )

Consequence

NPY2R-AS1
ENST00000511017.6 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.253

Variant links:

Genes affected

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

NPY2R-AS1 links:

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

MAP9-AS1 links:

NPY2R (HGNC:):

NPY2R links:

Genome browser will be placed here

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 = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPY2R-AS1	XR_001741894.2 linkuse as main transcript	n.149-77T>A		intron_variant, non_coding_transcript_variant
NPY2R	NM_001375470.1 linkuse as main transcript	c.-48-6000A>T		intron_variant			NP_001362399.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
NPY2R-AS1	ENST00000511017.6 linkuse as main transcript	n.329-77T>A	intron_variant, non_coding_transcript_variant	3
MAP9-AS1	ENST00000630664.2 linkuse as main transcript	n.208+33608A>T	intron_variant, non_coding_transcript_variant	5
NPY2R-AS1	ENST00000508687.1 linkuse as main transcript	n.219-77T>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15872

AN:

152022

Hom.:

979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0457

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.0746

Gnomad EAS

AF:

0.173

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.101

GnomAD4 exome

AF:

0.159

AC:

AN:

Hom.:

Cov.:

AF XY:

0.172

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.125

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.300

GnomAD4 genome

AF:

0.104

AC:

15874

AN:

152140

Hom.:

982

Cov.:

AF XY:

0.107

AC XY:

7973

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0458

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.0746

Gnomad4 EAS

AF:

0.172

Gnomad4 SAS

AF:

0.118

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.0998

Alfa

AF:

0.117

Hom.:

151

Bravo

AF:

0.102

Asia WGS

AF:

0.135

AC:

471

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

5.0

DANN

Benign

0.54

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