rs162430
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000592796.2(PYY):c.*64C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,590,194 control chromosomes in the GnomAD database, including 29,811 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.24 ( 6392 hom., cov: 32)
Exomes 𝑓: 0.14 ( 23419 hom. )
Consequence
PYY
ENST00000592796.2 3_prime_UTR
ENST00000592796.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0700
Genes affected
PYY (HGNC:9748): (peptide YY) This gene encodes a member of the neuropeptide Y (NPY) family of peptides. The encoded preproprotein is proteolytically processed to generate two alternative peptide products that differ in length by three amino acids. These peptides, secreted by endocrine cells in the gut, exhibit different binding affinities for each of the neuropeptide Y receptors. Binding of the encoded peptides to these receptors mediates regulation of pancreatic secretion, gut mobility and energy homeostasis. Rare variations in this gene could increase susceptibility to obesity and elevated serum levels of the encoded peptides may be associated with anorexia nervosa. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 17-43953041-G-A is Benign according to our data. Variant chr17-43953041-G-A is described in ClinVar as [Benign]. Clinvar id is 1243115.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYY | NM_001394028.1 | c.270-61C>T | intron_variant | ENST00000692052.1 | |||
PYY | NM_001394029.1 | c.*64C>T | 3_prime_UTR_variant | 3/3 | |||
PYY | NM_004160.6 | c.270-61C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYY | ENST00000592796.2 | c.*64C>T | 3_prime_UTR_variant | 3/3 | 1 | ||||
PYY | ENST00000692052.1 | c.270-61C>T | intron_variant | NM_001394028.1 | P1 | ||||
PYY | ENST00000360085.6 | c.270-61C>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.235 AC: 35699AN: 152060Hom.: 6348 Cov.: 32
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GnomAD4 exome AF: 0.135 AC: 194429AN: 1438016Hom.: 23419 Cov.: 31 AF XY: 0.137 AC XY: 97538AN XY: 713794
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GnomAD4 genome ? AF: 0.235 AC: 35804AN: 152178Hom.: 6392 Cov.: 32 AF XY: 0.240 AC XY: 17840AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | This variant is associated with the following publications: (PMID: 14551916) - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at