rs10488682
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000250018.6(TPH1):c.-173A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 687,316 control chromosomes in the GnomAD database, including 19,403 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 0.19 ( 3349 hom., cov: 32)
Exomes 𝑓: 0.24 ( 16054 hom. )
Consequence
TPH1
ENST00000250018.6 5_prime_UTR
ENST00000250018.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.603
Genes affected
TPH1 (HGNC:12008): (tryptophan hydroxylase 1) This gene encodes a member of the aromatic amino 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 have been associated with an elevated risk for a variety of diseases and disorders, including schizophrenia, somatic anxiety, anger-related traits, bipolar disorder, suicidal behavior, addictions, and others.[provided by RefSeq, Apr 2009]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPH1 | NM_004179.3 | c.-26-147A>T | intron_variant | ENST00000682019.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPH1 | ENST00000250018.6 | c.-173A>T | 5_prime_UTR_variant | 1/10 | 1 | P1 | |||
TPH1 | ENST00000682019.1 | c.-26-147A>T | intron_variant | NM_004179.3 | P1 | ||||
TPH1 | ENST00000528338.1 | c.5-147A>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.192 AC: 29126AN: 152018Hom.: 3347 Cov.: 32
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GnomAD4 exome AF: 0.237 AC: 126863AN: 535180Hom.: 16054 Cov.: 7 AF XY: 0.235 AC XY: 66434AN XY: 282218
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GnomAD4 genome ? AF: 0.191 AC: 29128AN: 152136Hom.: 3349 Cov.: 32 AF XY: 0.193 AC XY: 14337AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
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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