X-114731436-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000868.4(HTR2C):āc.178A>Gā(p.Ile60Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000181 in 110,738 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_000868.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.178A>G | p.Ile60Val | missense_variant | 4/6 | ENST00000276198.6 | |
LOC105373313 | XR_001755943.2 | n.574-660T>C | intron_variant, non_coding_transcript_variant | ||||
HTR2C | NM_001256760.3 | c.178A>G | p.Ile60Val | missense_variant | 5/7 | ||
HTR2C | NM_001256761.3 | c.178A>G | p.Ile60Val | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.178A>G | p.Ile60Val | missense_variant | 4/6 | 1 | NM_000868.4 | P1 | |
HTR2C | ENST00000371951.5 | c.178A>G | p.Ile60Val | missense_variant | 5/7 | 1 | P1 | ||
HTR2C | ENST00000371950.3 | c.178A>G | p.Ile60Val | missense_variant | 4/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000181 AC: 2AN: 110738Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32962
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.11e-7 AC: 1AN: 1097724Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363080
GnomAD4 genome AF: 0.0000181 AC: 2AN: 110738Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32962
ClinVar
Submissions by phenotype
HTR2C-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 22, 2023 | The HTR2C c.178A>G variant is predicted to result in the amino acid substitution p.Ile60Val. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at