chr11-113977551-A-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000869.6(HTR3A):c.68-220A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 1,548,166 control chromosomes in the GnomAD database, including 340,475 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 0.57 ( 26272 hom., cov: 32)
Exomes 𝑓: 0.67 ( 314203 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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR3A | NM_000869.6 | c.68-220A>T | intron_variant | ENST00000504030.7 | |||
HTR3A | NM_001161772.3 | c.-4A>T | 5_prime_UTR_variant | 1/9 | |||
HTR3A | NM_213621.4 | c.68-220A>T | intron_variant | ||||
HTR3A | NR_046363.2 | n.286-220A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR3A | ENST00000504030.7 | c.68-220A>T | intron_variant | 1 | NM_000869.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.568 AC: 86256AN: 151902Hom.: 26274 Cov.: 32
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GnomAD3 exomes AF: 0.626 AC: 96807AN: 154570Hom.: 31082 AF XY: 0.639 AC XY: 52356AN XY: 81898
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GnomAD4 exome AF: 0.667 AC: 931869AN: 1396146Hom.: 314203 Cov.: 34 AF XY: 0.670 AC XY: 461511AN XY: 688788
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GnomAD4 genome AF: 0.567 AC: 86264AN: 152020Hom.: 26272 Cov.: 32 AF XY: 0.567 AC XY: 42161AN XY: 74300
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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