rs2192372
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000868.4(HTR2C):c.-80+43414A>G 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 ( 16837 hom., 20887 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: -0.0400
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 Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BS2
?
High Homozygotes in GnomAd at 16847 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.-80+43414A>G | intron_variant | ENST00000276198.6 | |||
HTR2C | NM_001256760.3 | c.-171+43414A>G | intron_variant | ||||
HTR2C | NM_001256761.3 | c.-80+43414A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.-80+43414A>G | intron_variant | 1 | NM_000868.4 | P1 | |||
HTR2C | ENST00000371950.3 | c.-80+43414A>G | intron_variant | 1 | |||||
HTR2C | ENST00000371951.5 | c.-171+43414A>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.655 AC: 71668AN: 109371Hom.: 16847 Cov.: 22 AF XY: 0.655 AC XY: 20860AN XY: 31865
GnomAD3 genomes
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.655 AC: 71683AN: 109420Hom.: 16837 Cov.: 22 AF XY: 0.654 AC XY: 20887AN XY: 31924
GnomAD4 genome
?
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