rs756620309
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The ENST00000239461.11(PRRX1):c.343C>A(p.Arg115=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000239461.11 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRRX1 | NM_022716.4 | c.343C>A | p.Arg115= | synonymous_variant | 2/4 | ENST00000239461.11 | NP_073207.1 | |
PRRX1 | NM_006902.5 | c.343C>A | p.Arg115= | synonymous_variant | 2/5 | NP_008833.1 | ||
PRRX1 | XM_006711388.4 | c.202C>A | p.Arg68= | synonymous_variant | 3/5 | XP_006711451.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRRX1 | ENST00000239461.11 | c.343C>A | p.Arg115= | synonymous_variant | 2/4 | 1 | NM_022716.4 | ENSP00000239461 | P1 | |
PRRX1 | ENST00000367760.7 | c.343C>A | p.Arg115= | synonymous_variant | 2/5 | 1 | ENSP00000356734 | |||
PRRX1 | ENST00000497230.2 | c.343C>A | p.Arg115= | synonymous_variant | 2/3 | 2 | ENSP00000450762 | |||
PRRX1 | ENST00000553786.1 | n.453C>A | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251100Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135752
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at