rs6296
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000863.3(HTR1B):āc.861G>Cā(p.Val287=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,613,186 control chromosomes in the GnomAD database, including 63,939 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: š 0.27 ( 6034 hom., cov: 31)
Exomes š: 0.28 ( 57905 hom. )
Consequence
HTR1B
NM_000863.3 synonymous
NM_000863.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.298
Genes affected
HTR1B (HGNC:5287): (5-hydroxytryptamine receptor 1B) The protein encoded by this intronless gene is a G-protein coupled receptor for serotonin (5-hydroxytryptamine). Ligand binding activates second messengers that inhibit the activity of adenylate cyclase and manage the release of serotonin, dopamine, and acetylcholine in the brain. The encoded protein may be involved in several neuropsychiatric disorders and therefore is often a target of antidepressant and other psychotherapeutic drugs. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP7
?
Synonymous conserved (PhyloP=0.298 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR1B | NM_000863.3 | c.861G>C | p.Val287= | synonymous_variant | 1/1 | ENST00000369947.5 | |
LOC105377864 | XM_047419660.1 | c.-3742-11983C>G | intron_variant | ||||
LOC105377864 | XM_047419659.1 | c.-11681C>G | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR1B | ENST00000369947.5 | c.861G>C | p.Val287= | synonymous_variant | 1/1 | NM_000863.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.274 AC: 41648AN: 151758Hom.: 6038 Cov.: 31
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GnomAD3 exomes AF: 0.312 AC: 78305AN: 251170Hom.: 13200 AF XY: 0.309 AC XY: 41991AN XY: 135784
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GnomAD4 exome AF: 0.276 AC: 403965AN: 1461310Hom.: 57905 Cov.: 40 AF XY: 0.278 AC XY: 201882AN XY: 726962
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GnomAD4 genome ? AF: 0.274 AC: 41658AN: 151876Hom.: 6034 Cov.: 31 AF XY: 0.278 AC XY: 20659AN XY: 74218
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at