chrX-114584047-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The X-114584047-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 111,327 control chromosomes in the GnomAD database, including 762 homozygotes. There are 4,306 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.13 ( 761 hom., 4286 hem., cov: 21)
Exomes 𝑓: 0.16 ( 1 hom. 20 hem. )
Consequence
HTR2C
NM_000868.4 upstream_gene
NM_000868.4 upstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.695
Genes affected
HTR2C (HGNC:5295): (5-hydroxytryptamine receptor 2C) This gene encodes a seven-transmembrane G-protein-coupled receptor. The encoded protein responds to signaling through the neurotransmitter serotonin. The mRNA of this gene is subject to multiple RNA editing events, where adenosine residues encoded by the genome are converted to inosines. RNA editing is predicted to alter the structure of the second intracellular loop, thereby generating alternate protein forms with decreased ability to interact with G proteins. Abnormalities in RNA editing of this gene have been detected in victims of suicide that suffer from depression. In addition, naturally-occuring variation in the promoter and 5' non-coding and coding regions of this gene may show statistically-significant association with mental illness and behavioral disorders. Alternative splicing results in multiple different transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant X-114584047-C-T is Benign according to our data. Variant chrX-114584047-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 225992.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | upstream_gene_variant | ENST00000276198.6 | ||||
HTR2C | NM_001256760.3 | upstream_gene_variant | |||||
HTR2C | NM_001256761.3 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | upstream_gene_variant | 1 | NM_000868.4 | P1 | ||||
HTR2C | ENST00000371950.3 | upstream_gene_variant | 1 | ||||||
HTR2C | ENST00000371951.5 | upstream_gene_variant | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.127 AC: 14111AN: 110991Hom.: 762 Cov.: 21 AF XY: 0.129 AC XY: 4278AN XY: 33215
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GnomAD4 exome AF: 0.155 AC: 44AN: 283Hom.: 1 Cov.: 0 AF XY: 0.180 AC XY: 20AN XY: 111
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GnomAD4 genome AF: 0.127 AC: 14116AN: 111044Hom.: 761 Cov.: 21 AF XY: 0.129 AC XY: 4286AN XY: 33278
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 14, 2018 | This variant is associated with the following publications: (PMID: 15741483, 17376412, 21391883, 18192901, 19106782, 20010450, 20453482, 10768099) - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at