rs387906988
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_198859.4(PRICKLE2):c.443G>A(p.Arg148His) variant causes a missense change. The variant allele was found at a frequency of 0.00000684 in 1,461,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars). Synonymous variant affecting the same amino acid position (i.e. R148R) has been classified as Likely benign.
Frequency
Consequence
NM_198859.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRICKLE2 | NM_198859.4 | c.443G>A | p.Arg148His | missense_variant | 5/8 | ENST00000638394.2 | |
PRICKLE2 | NM_001370528.1 | c.443G>A | p.Arg148His | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRICKLE2 | ENST00000638394.2 | c.443G>A | p.Arg148His | missense_variant | 5/8 | 1 | NM_198859.4 | ||
PRICKLE2 | ENST00000295902.11 | c.611G>A | p.Arg204His | missense_variant | 6/9 | 5 | P1 | ||
PRICKLE2 | ENST00000564377.6 | c.443G>A | p.Arg148His | missense_variant | 5/8 | 5 | |||
PRICKLE2 | ENST00000640303.1 | n.1082G>A | non_coding_transcript_exon_variant | 3/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250150Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135418
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461580Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 727086
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at