rs6314
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000621.5(HTR2A):c.1354C>T(p.His452Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 1,613,530 control chromosomes in the GnomAD database, including 6,772 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H452P) has been classified as Uncertain significance.
Frequency
Consequence
NM_000621.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR2A | NM_000621.5 | c.1354C>T | p.His452Tyr | missense_variant | 4/4 | ENST00000542664.4 | |
HTR2A | NM_001378924.1 | c.1354C>T | p.His452Tyr | missense_variant | 4/4 | ||
HTR2A | NM_001165947.5 | c.865C>T | p.His289Tyr | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR2A | ENST00000542664.4 | c.1354C>T | p.His452Tyr | missense_variant | 4/4 | 1 | NM_000621.5 | P1 | |
HTR2A | ENST00000543956.5 | c.865C>T | p.His289Tyr | missense_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0931 AC: 14163AN: 152046Hom.: 717 Cov.: 32
GnomAD3 exomes AF: 0.0786 AC: 19741AN: 251056Hom.: 911 AF XY: 0.0804 AC XY: 10909AN XY: 135674
GnomAD4 exome AF: 0.0866 AC: 126548AN: 1461366Hom.: 6051 Cov.: 33 AF XY: 0.0874 AC XY: 63528AN XY: 727010
GnomAD4 genome ? AF: 0.0932 AC: 14182AN: 152164Hom.: 721 Cov.: 32 AF XY: 0.0913 AC XY: 6788AN XY: 74386
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at