chrX-114906816-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000868.4(HTR2C):c.778A>G(p.Ser260Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000902 in 1,208,748 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 29 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000868.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.778A>G | p.Ser260Gly | missense_variant | 6/6 | ENST00000276198.6 | |
HTR2C | NM_001256760.3 | c.778A>G | p.Ser260Gly | missense_variant | 7/7 | ||
HTR2C | NM_001256761.3 | c.683A>G | p.Lys228Arg | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.778A>G | p.Ser260Gly | missense_variant | 6/6 | 1 | NM_000868.4 | P1 | |
HTR2C | ENST00000371951.5 | c.778A>G | p.Ser260Gly | missense_variant | 7/7 | 1 | P1 | ||
HTR2C | ENST00000371950.3 | c.683A>G | p.Lys228Arg | missense_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000452 AC: 50AN: 110617Hom.: 0 Cov.: 22 AF XY: 0.000457 AC XY: 15AN XY: 32821
GnomAD3 exomes AF: 0.000147 AC: 27AN: 183211Hom.: 0 AF XY: 0.0000738 AC XY: 5AN XY: 67761
GnomAD4 exome AF: 0.0000537 AC: 59AN: 1098075Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 14AN XY: 363443
GnomAD4 genome ? AF: 0.000452 AC: 50AN: 110673Hom.: 0 Cov.: 22 AF XY: 0.000456 AC XY: 15AN XY: 32887
ClinVar
Submissions by phenotype
HTR2C-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 09, 2022 | 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