3-187698907-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001004312.2(RTP2):c.269G>A(p.Arg90His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,610,684 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004312.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RTP2 | NM_001004312.2 | c.269G>A | p.Arg90His | missense_variant | Exon 2 of 2 | ENST00000358241.1 | NP_001004312.2 | |
RTP2 | XM_017006301.2 | c.269G>A | p.Arg90His | missense_variant | Exon 5 of 5 | XP_016861790.1 | ||
RTP2 | XM_017006302.2 | c.269G>A | p.Arg90His | missense_variant | Exon 5 of 5 | XP_016861791.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248978Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134768
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1458396Hom.: 0 Cov.: 68 AF XY: 0.0000138 AC XY: 10AN XY: 724726
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.269G>A (p.R90H) alteration is located in exon 2 (coding exon 2) of the RTP2 gene. This alteration results from a G to A substitution at nucleotide position 269, causing the arginine (R) at amino acid position 90 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