12-112847722-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001143854.2(RPH3A):c.110C>A(p.Pro37His) variant causes a missense change. The variant allele was found at a frequency of 0.00015 in 1,613,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001143854.2 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 |
---|---|---|---|---|---|---|---|---|
RPH3A | NM_001143854.2 | c.110C>A | p.Pro37His | missense_variant | Exon 5 of 22 | ENST00000389385.9 | NP_001137326.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000251 AC: 63AN: 251236Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135770
GnomAD4 exome AF: 0.000150 AC: 219AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.000146 AC XY: 106AN XY: 727198
GnomAD4 genome AF: 0.000151 AC: 23AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74368
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.110C>A (p.P37H) alteration is located in exon 5 (coding exon 3) of the RPH3A gene. This alteration results from a C to A substitution at nucleotide position 110, causing the proline (P) at amino acid position 37 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