rs1058046
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001394028.1(PYY):āc.215C>Gā(p.Thr72Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 1,613,580 control chromosomes in the GnomAD database, including 349,468 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001394028.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYY | NM_001394028.1 | c.215C>G | p.Thr72Arg | missense_variant | 3/4 | ENST00000692052.1 | |
PYY | NM_004160.6 | c.215C>G | p.Thr72Arg | missense_variant | 6/7 | ||
PYY | NM_001394029.1 | c.215C>G | p.Thr72Arg | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYY | ENST00000692052.1 | c.215C>G | p.Thr72Arg | missense_variant | 3/4 | NM_001394028.1 | P1 | ||
PYY | ENST00000360085.6 | c.215C>G | p.Thr72Arg | missense_variant | 6/7 | 1 | P1 | ||
PYY | ENST00000592796.2 | c.215C>G | p.Thr72Arg | missense_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.594 AC: 90306AN: 151918Hom.: 27739 Cov.: 32
GnomAD3 exomes AF: 0.629 AC: 157612AN: 250384Hom.: 51111 AF XY: 0.641 AC XY: 86986AN XY: 135666
GnomAD4 exome AF: 0.659 AC: 963228AN: 1461544Hom.: 321719 Cov.: 68 AF XY: 0.662 AC XY: 481302AN XY: 727082
GnomAD4 genome ? AF: 0.594 AC: 90328AN: 152036Hom.: 27749 Cov.: 32 AF XY: 0.598 AC XY: 44403AN XY: 74310
ClinVar
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: 15983231) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at