rs2428712
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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.349+21437A>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 0.78 ( 24447 hom., 24167 hem., cov: 21)
Failed GnomAD Quality Control
Consequence
HTR2C
NM_000868.4 intron
NM_000868.4 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.313
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=-0.9).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.349+21437A>G | intron_variant | ENST00000276198.6 | NP_000859.2 | |||
HTR2C | NM_001256760.3 | c.349+21437A>G | intron_variant | NP_001243689.2 | ||||
HTR2C | NM_001256761.3 | c.349+21437A>G | intron_variant | NP_001243690.2 | ||||
LOC105373313 | XR_001755943.2 | n.574-22268T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.349+21437A>G | intron_variant | 1 | NM_000868.4 | ENSP00000276198.1 | ||||
HTR2C | ENST00000371951.5 | c.349+21437A>G | intron_variant | 1 | ENSP00000361019.1 | |||||
HTR2C | ENST00000371950.3 | c.349+21437A>G | intron_variant | 1 | ENSP00000361018.3 |
Frequencies
GnomAD3 genomes AF: 0.785 AC: 85055AN: 108366Hom.: 24460 Cov.: 21 AF XY: 0.787 AC XY: 24149AN XY: 30696
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: 0.785 AC: 85055AN: 108403Hom.: 24447 Cov.: 21 AF XY: 0.786 AC XY: 24167AN XY: 30743
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at