rs1386488
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173353.4(TPH2):c.608+1183C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 151,964 control chromosomes in the GnomAD database, including 48,325 homozygotes. 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 0.80 ( 48325 hom., cov: 30)
Consequence
TPH2
NM_173353.4 intron
NM_173353.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0660
Genes affected
TPH2 (HGNC:20692): (tryptophan hydroxylase 2) This gene encodes a member of the pterin-dependent aromatic acid hydroxylase family. The encoded protein catalyzes the first and rate limiting step in the biosynthesis of serotonin, an important hormone and neurotransmitter. Mutations in this gene may be associated with psychiatric diseases such as bipolar affective disorder and major depression. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPH2 | NM_173353.4 | c.608+1183C>A | intron_variant | ENST00000333850.4 | NP_775489.2 | |||
TPH2 | XR_001748575.2 | n.750+1183C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPH2 | ENST00000333850.4 | c.608+1183C>A | intron_variant | 1 | NM_173353.4 | ENSP00000329093.3 | ||||
TPH2 | ENST00000546576.1 | n.618+1183C>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.797 AC: 120978AN: 151846Hom.: 48278 Cov.: 30
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GnomAD4 genome AF: 0.797 AC: 121080AN: 151964Hom.: 48325 Cov.: 30 AF XY: 0.798 AC XY: 59267AN XY: 74276
GnomAD4 genome
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at