rs9764
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000909.6(NPY1R):c.*1050A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,466 control chromosomes in the GnomAD database, including 7,509 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 0.30 ( 7458 hom., cov: 32)
Exomes 𝑓: 0.43 ( 51 hom. )
Consequence
NPY1R
NM_000909.6 3_prime_UTR
NM_000909.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.39
Genes affected
NPY1R (HGNC:7956): (neuropeptide Y receptor Y1) This gene belongs to the G-protein-coupled receptor superfamily. The encoded transmembrane protein mediates the function of neuropeptide Y (NPY), a neurotransmitter, and peptide YY (PYY), a gastrointestinal hormone. The encoded receptor undergoes fast agonist-induced internalization through clathrin-coated pits and is subsequently recycled back to the cell membrane. Activation of Y1 receptors may result in mobilization of intracellular calcium and inhibition of adenylate cyclase activity. [provided by RefSeq, Aug 2013]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPY1R | NM_000909.6 | c.*1050A>G | 3_prime_UTR_variant | 3/3 | ENST00000296533.3 | ||
NPY1R | XM_005263031.5 | c.*1050A>G | 3_prime_UTR_variant | 3/3 | |||
NPY1R | XM_011532010.4 | c.*1050A>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPY1R | ENST00000296533.3 | c.*1050A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_000909.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.304 AC: 46194AN: 151916Hom.: 7449 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.428 AC: 185AN: 432Hom.: 51 Cov.: 0 AF XY: 0.423 AC XY: 110AN XY: 260
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GnomAD4 genome ? AF: 0.304 AC: 46232AN: 152034Hom.: 7458 Cov.: 32 AF XY: 0.307 AC XY: 22852AN XY: 74320
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at