rs1460470110
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000317.3(PTS):c.9G>A(p.Thr3Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000021 in 1,428,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PTS
NM_000317.3 synonymous
NM_000317.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.346
Publications
0 publications found
Genes affected
PTS (HGNC:9689): (6-pyruvoyltetrahydropterin synthase) The enzyme encoded by this gene catalyzes the elimination of inorganic triphosphate from dihydroneopterin triphosphate, which is the second and irreversible step in the biosynthesis of tetrahydrobiopterin from GTP. Tetrahydrobiopterin, also known as BH(4), is an essential cofactor and regulator of various enzyme activities, including enzymes involved in serotonin biosynthesis and NO synthase activity. Mutations in this gene result in hyperphenylalaninemia. [provided by RefSeq, Oct 2008]
PTS Gene-Disease associations (from GenCC):
- BH4-deficient hyperphenylalaninemia AInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 11-112226452-G-A is Benign according to our data. Variant chr11-112226452-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1641671.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.346 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000210 AC: 3AN: 1428092Hom.: 0 Cov.: 31 AF XY: 0.00000141 AC XY: 1AN XY: 706952 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1428092
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
706952
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33264
American (AMR)
AF:
AC:
0
AN:
37442
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25364
East Asian (EAS)
AF:
AC:
0
AN:
38602
South Asian (SAS)
AF:
AC:
0
AN:
81392
European-Finnish (FIN)
AF:
AC:
0
AN:
49736
Middle Eastern (MID)
AF:
AC:
0
AN:
5614
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1097338
Other (OTH)
AF:
AC:
0
AN:
59340
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.442
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
6-Pyruvoyl-tetrahydrobiopterin synthase deficiency Benign:1
Sep 17, 2021
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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