3-11259200-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001098212.2(HRH1):c.163G>A(p.Glu55Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098212.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HRH1 | NM_001098212.2 | c.163G>A | p.Glu55Lys | missense_variant | 2/2 | ENST00000431010.3 | |
HRH1 | NM_000861.3 | c.163G>A | p.Glu55Lys | missense_variant | 3/3 | ||
HRH1 | NM_001098211.2 | c.163G>A | p.Glu55Lys | missense_variant | 2/2 | ||
HRH1 | NM_001098213.2 | c.163G>A | p.Glu55Lys | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HRH1 | ENST00000431010.3 | c.163G>A | p.Glu55Lys | missense_variant | 2/2 | 1 | NM_001098212.2 | P1 | |
HRH1 | ENST00000397056.1 | c.163G>A | p.Glu55Lys | missense_variant | 3/3 | 1 | P1 | ||
HRH1 | ENST00000438284.2 | c.163G>A | p.Glu55Lys | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461880Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727242
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2023 | The c.163G>A (p.E55K) alteration is located in exon 2 (coding exon 1) of the HRH1 gene. This alteration results from a G to A substitution at nucleotide position 163, causing the glutamic acid (E) at amino acid position 55 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.