chr11-113946042-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006028.5(HTR3B):c.1231C>T(p.Arg411Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R411H) has been classified as Uncertain significance.
Frequency
Consequence
NM_006028.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR3B | NM_006028.5 | c.1231C>T | p.Arg411Cys | missense_variant | 9/9 | ENST00000260191.8 | |
HTR3B | NM_001363563.2 | c.1198C>T | p.Arg400Cys | missense_variant | 8/8 | ||
HTR3B | XM_017018552.3 | c.1024C>T | p.Arg342Cys | missense_variant | 8/8 | ||
HTR3B | XM_024448767.2 | c.937C>T | p.Arg313Cys | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR3B | ENST00000260191.8 | c.1231C>T | p.Arg411Cys | missense_variant | 9/9 | 1 | NM_006028.5 | P2 | |
HTR3B | ENST00000537778.5 | c.1198C>T | p.Arg400Cys | missense_variant | 8/8 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 251094Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135702
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.0000605 AC XY: 44AN XY: 727224
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.1231C>T (p.R411C) alteration is located in exon 9 (coding exon 9) of the HTR3B gene. This alteration results from a C to T substitution at nucleotide position 1231, causing the arginine (R) at amino acid position 411 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at