rs12838742
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000868.4(HTR2C):c.-80+4872C>T 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 0.66 ( 17262 hom., 21248 hem., cov: 22)
Failed GnomAD Quality Control
Consequence
HTR2C
NM_000868.4 intron
NM_000868.4 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00200
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 -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.-80+4872C>T | intron_variant | ENST00000276198.6 | |||
HTR2C | NM_001256760.3 | c.-171+4872C>T | intron_variant | ||||
HTR2C | NM_001256761.3 | c.-80+4872C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.-80+4872C>T | intron_variant | 1 | NM_000868.4 | P1 | |||
HTR2C | ENST00000371950.3 | c.-80+4872C>T | intron_variant | 1 | |||||
HTR2C | ENST00000371951.5 | c.-171+4872C>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.663 AC: 72815AN: 109861Hom.: 17270 Cov.: 22 AF XY: 0.661 AC XY: 21228AN XY: 32137
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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: 0.663 AC: 72826AN: 109910Hom.: 17262 Cov.: 22 AF XY: 0.660 AC XY: 21248AN XY: 32194
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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