rs778536806
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003857.4(GALR2):āc.127A>Cā(p.Asn43His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 1,608,844 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 (ā ).
Frequency
Consequence
NM_003857.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALR2 | NM_003857.4 | c.127A>C | p.Asn43His | missense_variant | Exon 1 of 2 | ENST00000329003.4 | NP_003848.1 | |
GALR2 | XM_011525427.4 | c.76-120A>C | intron_variant | Intron 2 of 3 | XP_011523729.1 | |||
GALR2 | XM_047436984.1 | c.76-120A>C | intron_variant | Intron 2 of 3 | XP_047292940.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000101 AC: 25AN: 247468Hom.: 0 AF XY: 0.000134 AC XY: 18AN XY: 134418
GnomAD4 exome AF: 0.000133 AC: 194AN: 1456708Hom.: 0 Cov.: 32 AF XY: 0.000128 AC XY: 93AN XY: 724894
GnomAD4 genome AF: 0.000112 AC: 17AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.127A>C (p.N43H) alteration is located in exon 1 (coding exon 1) of the GALR2 gene. This alteration results from a A to C substitution at nucleotide position 127, causing the asparagine (N) at amino acid position 43 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