12-49295263-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_006262.4(PRPH):c.63C>T(p.Phe21Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0177 in 1,611,846 control chromosomes in the GnomAD database, including 306 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006262.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRPH | ENST00000257860.9 | c.63C>T | p.Phe21Phe | synonymous_variant | Exon 1 of 9 | 1 | NM_006262.4 | ENSP00000257860.4 | ||
TROAP-AS1 | ENST00000553259.1 | n.2809G>A | non_coding_transcript_exon_variant | Exon 6 of 8 | 2 | |||||
PRPH | ENST00000451891.4 | c.-181C>T | upstream_gene_variant | 5 | ENSP00000408897.4 |
Frequencies
GnomAD3 genomes AF: 0.0211 AC: 3218AN: 152218Hom.: 33 Cov.: 33
GnomAD3 exomes AF: 0.0226 AC: 5398AN: 238442Hom.: 91 AF XY: 0.0224 AC XY: 2928AN XY: 130602
GnomAD4 exome AF: 0.0173 AC: 25235AN: 1459510Hom.: 269 Cov.: 31 AF XY: 0.0173 AC XY: 12573AN XY: 725992
GnomAD4 genome AF: 0.0213 AC: 3246AN: 152336Hom.: 37 Cov.: 33 AF XY: 0.0218 AC XY: 1627AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:2Other:1
- -
- -
- -
PRPH-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at