rs543229
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000868.4(HTR2C):c.-147+1854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 ( 24934 hom., 26307 hem., cov: 23)
Failed GnomAD Quality Control
Consequence
HTR2C
NM_000868.4 intron
NM_000868.4 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.41
Genes affected
HTR2C (HGNC:5295): (5-hydroxytryptamine receptor 2C) This gene encodes a seven-transmembrane G-protein-coupled receptor. The encoded protein responds to signaling through the neurotransmitter serotonin. The mRNA of this gene is subject to multiple RNA editing events, where adenosine residues encoded by the genome are converted to inosines. RNA editing is predicted to alter the structure of the second intracellular loop, thereby generating alternate protein forms with decreased ability to interact with G proteins. Abnormalities in RNA editing of this gene have been detected in victims of suicide that suffer from depression. In addition, naturally-occuring variation in the promoter and 5' non-coding and coding regions of this gene may show statistically-significant association with mental illness and behavioral disorders. Alternative splicing results in multiple different transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.-147+1854G>A | intron_variant | ENST00000276198.6 | |||
HTR2C | NM_001256760.3 | c.-238+1854G>A | intron_variant | ||||
HTR2C | NM_001256761.3 | c.-147+1854G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.-147+1854G>A | intron_variant | 1 | NM_000868.4 | P1 | |||
HTR2C | ENST00000371950.3 | c.-147+1854G>A | intron_variant | 1 | |||||
HTR2C | ENST00000371951.5 | c.-238+1854G>A | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.800 AC: 88281AN: 110317Hom.: 24946 Cov.: 23 AF XY: 0.808 AC XY: 26280AN XY: 32531
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.800 AC: 88287AN: 110367Hom.: 24934 Cov.: 23 AF XY: 0.807 AC XY: 26307AN XY: 32591
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at