rs6320
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_024012.4(HTR5A):c.12T>A(p.Pro4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 1,600,956 control chromosomes in the GnomAD database, including 65,314 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 0.26 ( 5281 hom., cov: 32)
Exomes 𝑓: 0.28 ( 60033 hom. )
Consequence
HTR5A
NM_024012.4 synonymous
NM_024012.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.736
Genes affected
HTR5A (HGNC:5300): (5-hydroxytryptamine receptor 5A) The neurotransmitter serotonin (5-hydroxytryptamine, 5-HT) has been implicated in a wide range of psychiatric conditions and also has vasoconstrictive and vasodilatory effects. The gene described in this record is a member of 5-hydroxytryptamine (serotonin) receptor family and encodes a multi-pass membrane protein that functions as a receptor for 5-hydroxytryptamine and couples to G-proteins. This protein has been shown to function in part through the regulation of intracellular Ca2+ mobilization. [provided by RefSeq, Jul 2008]
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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=-0.74).
BP7
?
Synonymous conserved (PhyloP=-0.736 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR5A | NM_024012.4 | c.12T>A | p.Pro4= | synonymous_variant | 1/2 | ENST00000287907.3 | |
HTR5A-AS1 | NR_038945.1 | n.524+123A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR5A | ENST00000287907.3 | c.12T>A | p.Pro4= | synonymous_variant | 1/2 | 1 | NM_024012.4 | P1 | |
HTR5A-AS1 | ENST00000671665.1 | n.1417+123A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.259 AC: 39345AN: 151972Hom.: 5281 Cov.: 32
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GnomAD3 exomes AF: 0.262 AC: 63551AN: 242472Hom.: 8692 AF XY: 0.262 AC XY: 34548AN XY: 131694
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GnomAD4 exome AF: 0.285 AC: 412353AN: 1448866Hom.: 60033 Cov.: 42 AF XY: 0.283 AC XY: 204262AN XY: 720934
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GnomAD4 genome ? AF: 0.259 AC: 39366AN: 152090Hom.: 5281 Cov.: 32 AF XY: 0.257 AC XY: 19137AN XY: 74346
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at