chr17-43953963-C-G

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.307

Publications

16 publications found
Variant links:
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
PYYNM_004160.6 linkc.-114G>C 5_prime_UTR_variant Exon 4 of 7 NP_004151.4 P10082-1
PYYNM_001394028.1 linkc.-114G>C upstream_gene_variant ENST00000692052.1 NP_001380957.1
PYYNM_001394029.1 linkc.-114G>C upstream_gene_variant NP_001380958.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PYYENST00000360085.6 linkc.-114G>C 5_prime_UTR_variant Exon 4 of 7 1 ENSP00000353198.1 P10082-1
PYYENST00000692052.1 linkc.-114G>C upstream_gene_variant NM_001394028.1 ENSP00000509262.1 P10082-1
PYYENST00000592796.2 linkc.-114G>C upstream_gene_variant 1 ENSP00000467310.1 P10082-2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151916
Hom.:
0
Cov.:
31
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
2302
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
1196
African (AFR)
AF:
0.00
AC:
0
AN:
62
American (AMR)
AF:
0.00
AC:
0
AN:
16
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16
East Asian (EAS)
AF:
0.00
AC:
0
AN:
20
South Asian (SAS)
AF:
0.00
AC:
0
AN:
62
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
424
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1122
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
428
Other (OTH)
AF:
0.00
AC:
0
AN:
152
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
151916
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
74184
African (AFR)
AF:
0.00
AC:
0
AN:
41374
American (AMR)
AF:
0.00
AC:
0
AN:
15250
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3466
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5170
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10560
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67952
Other (OTH)
AF:
0.00
AC:
0
AN:
2090
Alfa
AF:
0.00
Hom.:
92476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.26
CADD
Benign
17
DANN
Benign
0.87
PhyloP100
-0.31
PromoterAI
-0.16
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2070592; hg19: chr17-42031331; API