17-76076815-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003857.4(GALR2):c.548G>A(p.Arg183His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000436 in 1,605,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003857.4 missense
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 |
---|---|---|---|---|---|---|---|---|
GALR2 | NM_003857.4 | c.548G>A | p.Arg183His | missense_variant | Exon 2 of 2 | ENST00000329003.4 | NP_003848.1 | |
GALR2 | XM_011525427.4 | c.377G>A | p.Arg126His | missense_variant | Exon 4 of 4 | XP_011523729.1 | ||
GALR2 | XM_047436984.1 | c.377G>A | p.Arg126His | missense_variant | Exon 4 of 4 | XP_047292940.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000702 AC: 17AN: 242240Hom.: 0 AF XY: 0.0000377 AC XY: 5AN XY: 132512
GnomAD4 exome AF: 0.0000248 AC: 36AN: 1453086Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 723252
GnomAD4 genome AF: 0.000223 AC: 34AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.548G>A (p.R183H) alteration is located in exon 2 (coding exon 2) of the GALR2 gene. This alteration results from a G to A substitution at nucleotide position 548, causing the arginine (R) at amino acid position 183 to be replaced by a histidine (H). 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