rs12512687

Variant summary

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

The XM_005263038.4(NPY5R):​c.*433G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 156,200 control chromosomes in the GnomAD database, including 553 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 0.079 ( 539 hom., cov: 33)
Exomes 𝑓: 0.084 ( 14 hom. )

Consequence

NPY5R
XM_005263038.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25
Variant links:
Genes affected
NPY5R (HGNC:7958): (neuropeptide Y receptor Y5) The protein encoded by this gene is a receptor for neuropeptide Y and peptide YY. The encoded protein appears to be involved in regulating food intake, with defects in this gene being associated with eating disorders. Also, the encoded protein is involved in a pathway that protects neuroblastoma cells from chemotherapy-induced cell death, providing a possible therapeutic target against neuroblastoma. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Nov 2015]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NPY5RNM_006174.4 linkc.*433G>A downstream_gene_variant ENST00000338566.8 NP_006165.1 Q15761

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NPY5RENST00000338566.8 linkc.*433G>A downstream_gene_variant 1 NM_006174.4 ENSP00000339377.3 Q15761
NPY5RENST00000515560.1 linkc.*433G>A downstream_gene_variant 2 ENSP00000423917.1 Q15761

Frequencies

GnomAD3 genomes
AF:
0.0795
AC:
12082
AN:
151930
Hom.:
543
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0773
Gnomad AMI
AF:
0.0340
Gnomad AMR
AF:
0.0947
Gnomad ASJ
AF:
0.0664
Gnomad EAS
AF:
0.142
Gnomad SAS
AF:
0.178
Gnomad FIN
AF:
0.0821
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0668
Gnomad OTH
AF:
0.0755
GnomAD4 exome
AF:
0.0838
AC:
348
AN:
4152
Hom.:
14
AF XY:
0.0817
AC XY:
175
AN XY:
2142
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.100
Gnomad4 ASJ exome
AF:
0.0625
Gnomad4 EAS exome
AF:
0.0625
Gnomad4 SAS exome
AF:
0.286
Gnomad4 FIN exome
AF:
0.0881
Gnomad4 NFE exome
AF:
0.0357
Gnomad4 OTH exome
AF:
0.0500
GnomAD4 genome
AF:
0.0794
AC:
12075
AN:
152048
Hom.:
539
Cov.:
33
AF XY:
0.0814
AC XY:
6046
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.0772
Gnomad4 AMR
AF:
0.0948
Gnomad4 ASJ
AF:
0.0664
Gnomad4 EAS
AF:
0.141
Gnomad4 SAS
AF:
0.177
Gnomad4 FIN
AF:
0.0821
Gnomad4 NFE
AF:
0.0669
Gnomad4 OTH
AF:
0.0747
Alfa
AF:
0.0343
Hom.:
26
Bravo
AF:
0.0817
Asia WGS
AF:
0.148
AC:
513
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.35
DANN
Benign
0.44

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.

Other links and lift over

dbSNP: rs12512687; hg19: chr4-164273196; API