rs12288145
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006028.5(HTR3B):c.907+118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0383 in 807,448 control chromosomes in the GnomAD database, including 709 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 0.033 ( 102 hom., cov: 32)
Exomes 𝑓: 0.040 ( 607 hom. )
Consequence
HTR3B
NM_006028.5 intron
NM_006028.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.163
Genes affected
HTR3B (HGNC:5298): (5-hydroxytryptamine receptor 3B) The product of this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit B of the type 3 receptor for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. This receptor causes fast, depolarizing responses in neurons after activation. It is not functional as a homomeric complex, but a pentaheteromeric complex with subunit A (HTR3A) displays the full functional features of this receptor. [provided by RefSeq, Aug 2011]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0543 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR3B | NM_006028.5 | c.907+118G>A | intron_variant | ENST00000260191.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR3B | ENST00000260191.8 | c.907+118G>A | intron_variant | 1 | NM_006028.5 | P2 | |||
HTR3B | ENST00000537778.5 | c.874+118G>A | intron_variant | 1 | A2 | ||||
HTR3B | ENST00000543092.1 | c.483-1263G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0327 AC: 4979AN: 152070Hom.: 99 Cov.: 32
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GnomAD4 exome AF: 0.0395 AC: 25911AN: 655260Hom.: 607 AF XY: 0.0415 AC XY: 14240AN XY: 343148
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GnomAD4 genome ? AF: 0.0327 AC: 4984AN: 152188Hom.: 102 Cov.: 32 AF XY: 0.0317 AC XY: 2359AN XY: 74400
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at