20-62219906-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007232.3(HRH3):c.65C>T(p.Ala22Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000565 in 1,344,326 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 (★).
Frequency
Consequence
NM_007232.3 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 |
---|---|---|---|---|---|---|---|
HRH3 | NM_007232.3 | c.65C>T | p.Ala22Val | missense_variant | 1/3 | ENST00000340177.10 | |
HRH3 | XM_005260266.4 | c.65C>T | p.Ala22Val | missense_variant | 1/4 | ||
HRH3 | XM_017027623.2 | c.65C>T | p.Ala22Val | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HRH3 | ENST00000340177.10 | c.65C>T | p.Ala22Val | missense_variant | 1/3 | 1 | NM_007232.3 | P1 | |
HRH3 | ENST00000317393.10 | c.65C>T | p.Ala22Val | missense_variant | 1/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000321 AC: 48AN: 149732Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000243 AC: 29AN: 1194484Hom.: 0 Cov.: 30 AF XY: 0.0000154 AC XY: 9AN XY: 583300
GnomAD4 genome ? AF: 0.000314 AC: 47AN: 149842Hom.: 0 Cov.: 32 AF XY: 0.000301 AC XY: 22AN XY: 73146
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 07, 2022 | The c.65C>T (p.A22V) alteration is located in exon 1 (coding exon 1) of the HRH3 gene. This alteration results from a C to T substitution at nucleotide position 65, causing the alanine (A) at amino acid position 22 to be replaced by a valine (V). 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