rs1985242
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000869.6(HTR3A):c.68-220A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000206 in 1,549,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
HTR3A
NM_000869.6 intron
NM_000869.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.743
Genes affected
HTR3A (HGNC:5297): (5-hydroxytryptamine receptor 3A) The product of this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit A 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 appears that the heteromeric combination of A and B subunits is necessary to provide the full functional features of this receptor, since either subunit alone results in receptors with very low conductance and response amplitude. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR3A | NM_000869.6 | c.68-220A>C | intron_variant | ENST00000504030.7 | |||
HTR3A | NM_001161772.3 | c.-4A>C | 5_prime_UTR_variant | 1/9 | |||
HTR3A | NM_213621.4 | c.68-220A>C | intron_variant | ||||
HTR3A | NR_046363.2 | n.286-220A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR3A | ENST00000504030.7 | c.68-220A>C | intron_variant | 1 | NM_000869.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 151962Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000259 AC: 4AN: 154570Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81898
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GnomAD4 exome AF: 0.0000129 AC: 18AN: 1397878Hom.: 0 Cov.: 34 AF XY: 0.0000102 AC XY: 7AN XY: 689574
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GnomAD4 genome AF: 0.0000921 AC: 14AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.0000943 AC XY: 7AN XY: 74208
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at