12-42460111-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_153026.3(PRICKLE1):c.2194G>A(p.Gly732Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_153026.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRICKLE1 | NM_153026.3 | c.2194G>A | p.Gly732Arg | missense_variant | 8/8 | ENST00000345127.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRICKLE1 | ENST00000345127.9 | c.2194G>A | p.Gly732Arg | missense_variant | 8/8 | 1 | NM_153026.3 | P1 | |
ENST00000547824.1 | n.746C>T | non_coding_transcript_exon_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000263 AC: 66AN: 251228Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135784
GnomAD4 exome AF: 0.000104 AC: 152AN: 1461856Hom.: 0 Cov.: 34 AF XY: 0.000109 AC XY: 79AN XY: 727228
GnomAD4 genome AF: 0.000145 AC: 22AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74404
ClinVar
Submissions by phenotype
Epilepsy, progressive myoclonic, 1B Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at