rs17110566
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173353.4(TPH2):c.805+152G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 794,336 control chromosomes in the GnomAD database, including 1,225 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 0.040 ( 270 hom., cov: 32)
Exomes 𝑓: 0.041 ( 955 hom. )
Consequence
TPH2
NM_173353.4 intron
NM_173353.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.127
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPH2 | NM_173353.4 | c.805+152G>A | intron_variant | ENST00000333850.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPH2 | ENST00000333850.4 | c.805+152G>A | intron_variant | 1 | NM_173353.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0403 AC: 6123AN: 152114Hom.: 264 Cov.: 32
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GnomAD4 exome AF: 0.0407 AC: 26118AN: 642104Hom.: 955 AF XY: 0.0394 AC XY: 13325AN XY: 337932
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GnomAD4 genome ? AF: 0.0403 AC: 6129AN: 152232Hom.: 270 Cov.: 32 AF XY: 0.0457 AC XY: 3400AN XY: 74430
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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