rs6316
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001378924.1(HTR2A):c.-328-854A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0116 in 440,608 control chromosomes in the GnomAD database, including 220 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 0.027 ( 189 hom., cov: 32)
Exomes 𝑓: 0.0032 ( 31 hom. )
Consequence
HTR2A
NM_001378924.1 intron
NM_001378924.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.48
Genes affected
HTR2A (HGNC:5293): (5-hydroxytryptamine receptor 2A) This gene encodes one of the receptors for serotonin, a neurotransmitter with many roles. Mutations in this gene are associated with susceptibility to schizophrenia and obsessive-compulsive disorder, and are also associated with response to the antidepressant citalopram in patients with major depressive disorder (MDD). MDD patients who also have a mutation in intron 2 of this gene show a significantly reduced response to citalopram as this antidepressant downregulates expression of this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 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=-0.54).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.094 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2A | NM_001378924.1 | c.-328-854A>G | intron_variant | ||||
HTR2A | NM_000621.5 | upstream_gene_variant | ENST00000542664.4 | ||||
HTR2A | NM_001165947.5 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2A | ENST00000542664.4 | upstream_gene_variant | 1 | NM_000621.5 | P1 | ||||
HTR2A | ENST00000543956.5 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0275 AC: 4180AN: 152140Hom.: 189 Cov.: 32
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GnomAD4 exome AF: 0.00323 AC: 932AN: 288350Hom.: 31 Cov.: 0 AF XY: 0.00281 AC XY: 423AN XY: 150414
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GnomAD4 genome ? AF: 0.0275 AC: 4185AN: 152258Hom.: 189 Cov.: 32 AF XY: 0.0268 AC XY: 1996AN XY: 74456
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at