chr17-43953963-C-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The ENST00000360085.6(PYY):c.-114G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PYY
ENST00000360085.6 5_prime_UTR
ENST00000360085.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.307
Publications
16 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PYY | NM_004160.6 | c.-114G>C | 5_prime_UTR_variant | Exon 4 of 7 | NP_004151.4 | |||
PYY | NM_001394028.1 | c.-114G>C | upstream_gene_variant | ENST00000692052.1 | NP_001380957.1 | |||
PYY | NM_001394029.1 | c.-114G>C | upstream_gene_variant | NP_001380958.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PYY | ENST00000360085.6 | c.-114G>C | 5_prime_UTR_variant | Exon 4 of 7 | 1 | ENSP00000353198.1 | ||||
PYY | ENST00000692052.1 | c.-114G>C | upstream_gene_variant | NM_001394028.1 | ENSP00000509262.1 | |||||
PYY | ENST00000592796.2 | c.-114G>C | upstream_gene_variant | 1 | ENSP00000467310.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151916Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
0
AN:
151916
Hom.:
Cov.:
31
Gnomad AFR
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Gnomad OTH
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2302Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 1196
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
2302
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
1196
African (AFR)
AF:
AC:
0
AN:
62
American (AMR)
AF:
AC:
0
AN:
16
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
16
East Asian (EAS)
AF:
AC:
0
AN:
20
South Asian (SAS)
AF:
AC:
0
AN:
62
European-Finnish (FIN)
AF:
AC:
0
AN:
424
Middle Eastern (MID)
AF:
AC:
0
AN:
1122
European-Non Finnish (NFE)
AF:
AC:
0
AN:
428
Other (OTH)
AF:
AC:
0
AN:
152
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151916Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74184
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151916
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74184
African (AFR)
AF:
AC:
0
AN:
41374
American (AMR)
AF:
AC:
0
AN:
15250
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5170
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10560
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67952
Other (OTH)
AF:
AC:
0
AN:
2090
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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