rs1414334
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000868.4(HTR2C):c.551-3008C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.78 ( 23868 hom., 26246 hem., cov: 24)
Failed GnomAD Quality Control
Consequence
HTR2C
NM_000868.4 intron
NM_000868.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0280
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant X-114903581-C-G is Benign according to our data. Variant chrX-114903581-C-G is described in ClinVar as [Benign]. Clinvar id is 225952.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-114903581-C-G is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.551-3008C>G | intron_variant | ENST00000276198.6 | |||
HTR2C | NM_001256760.3 | c.551-3008C>G | intron_variant | ||||
HTR2C | NM_001256761.3 | c.456-3008C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.551-3008C>G | intron_variant | 1 | NM_000868.4 | P1 | |||
HTR2C | ENST00000371950.3 | c.456-3008C>G | intron_variant | 1 | |||||
HTR2C | ENST00000371951.5 | c.551-3008C>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.775 AC: 86188AN: 111142Hom.: 23880 Cov.: 24 AF XY: 0.787 AC XY: 26229AN XY: 33346
GnomAD3 genomes
?
AF:
AC:
86188
AN:
111142
Hom.:
Cov.:
24
AF XY:
AC XY:
26229
AN XY:
33346
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.775 AC: 86185AN: 111195Hom.: 23868 Cov.: 24 AF XY: 0.786 AC XY: 26246AN XY: 33409
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
86185
AN:
111195
Hom.:
Cov.:
24
AF XY:
AC XY:
26246
AN XY:
33409
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 09, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at