12-49295304-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006262.4(PRPH):c.104C>G(p.Ser35Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000478 in 1,611,542 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006262.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRPH | ENST00000257860.9 | c.104C>G | p.Ser35Trp | missense_variant | Exon 1 of 9 | 1 | NM_006262.4 | ENSP00000257860.4 | ||
TROAP-AS1 | ENST00000553259.1 | n.2768G>C | non_coding_transcript_exon_variant | Exon 6 of 8 | 2 | |||||
PRPH | ENST00000451891.4 | c.-140C>G | upstream_gene_variant | 5 | ENSP00000408897.4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000337 AC: 8AN: 237632Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130394
GnomAD4 exome AF: 0.0000521 AC: 76AN: 1459302Hom.: 0 Cov.: 31 AF XY: 0.0000496 AC XY: 36AN XY: 725876
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.104C>G (p.S35W) alteration is located in exon 1 (coding exon 1) of the PRPH gene. This alteration results from a C to G substitution at nucleotide position 104, causing the serine (S) at amino acid position 35 to be replaced by a tryptophan (W). 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