chrX-114906698-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The ENST00000371950.3(HTR2C):c.565C>T(p.Arg189Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,208,785 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000371950.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.660C>T | p.Phe220= | synonymous_variant | 6/6 | ENST00000276198.6 | |
HTR2C | NM_001256761.3 | c.565C>T | p.Arg189Cys | missense_variant | 6/6 | ||
HTR2C | NM_001256760.3 | c.660C>T | p.Phe220= | synonymous_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000371950.3 | c.565C>T | p.Arg189Cys | missense_variant | 6/6 | 1 | |||
HTR2C | ENST00000276198.6 | c.660C>T | p.Phe220= | synonymous_variant | 6/6 | 1 | NM_000868.4 | P1 | |
HTR2C | ENST00000371951.5 | c.660C>T | p.Phe220= | synonymous_variant | 7/7 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 111117Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33331
GnomAD3 exomes AF: 0.0000546 AC: 10AN: 183247Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67745
GnomAD4 exome AF: 0.0000191 AC: 21AN: 1097613Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 3AN XY: 362989
GnomAD4 genome ? AF: 0.0000180 AC: 2AN: 111172Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33396
ClinVar
Submissions by phenotype
HTR2C-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 17, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at