rs62625041
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_000869.6(HTR3A):c.-25C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00134 in 1,612,804 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0014 ( 2 hom. )
Consequence
HTR3A
NM_000869.6 5_prime_UTR
NM_000869.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.496
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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 11-113975301-C-T is Benign according to our data. Variant chr11-113975301-C-T is described in Lovd as [Likely_benign].
BS2
?
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR3A | NM_000869.6 | c.-25C>T | 5_prime_UTR_variant | 1/9 | ENST00000504030.7 | ||
HTR3A | NM_213621.4 | c.-25C>T | 5_prime_UTR_variant | 1/8 | |||
HTR3A | NR_046363.2 | n.194C>T | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR3A | ENST00000504030.7 | c.-25C>T | 5_prime_UTR_variant | 1/9 | 1 | NM_000869.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000795 AC: 121AN: 152228Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000818 AC: 204AN: 249390Hom.: 0 AF XY: 0.000816 AC XY: 110AN XY: 134884
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GnomAD4 exome AF: 0.00140 AC: 2041AN: 1460458Hom.: 2 Cov.: 33 AF XY: 0.00134 AC XY: 972AN XY: 726504
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GnomAD4 genome ? AF: 0.000794 AC: 121AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.000604 AC XY: 45AN XY: 74496
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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