rs3813929
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000868.4(HTR2C):c.-759C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 111,000 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000868.4 upstream_gene
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HTR2C | NM_000868.4 | c.-759C>G | upstream_gene_variant | ENST00000276198.6 | NP_000859.2 | |||
HTR2C | NM_001256760.3 | c.-850C>G | upstream_gene_variant | NP_001243689.2 | ||||
HTR2C | NM_001256761.3 | c.-759C>G | upstream_gene_variant | NP_001243690.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HTR2C | ENST00000276198.6 | c.-759C>G | upstream_gene_variant | 1 | NM_000868.4 | ENSP00000276198.1 | ||||
HTR2C | ENST00000371951.5 | c.-850C>G | upstream_gene_variant | 1 | ENSP00000361019.1 | |||||
HTR2C | ENST00000371950.3 | c.-759C>G | upstream_gene_variant | 1 | ENSP00000361018.3 |
Frequencies
GnomAD3 genomes AF: 0.0000180 AC: 2AN: 111000Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33222
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 287Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 113
GnomAD4 genome AF: 0.0000180 AC: 2AN: 111000Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 33222
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at