12-42460406-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_153026.3(PRICKLE1):c.1899T>C(p.Phe633Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 1,613,382 control chromosomes in the GnomAD database, including 104,864 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_153026.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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PRICKLE1 | NM_153026.3 | c.1899T>C | p.Phe633Phe | synonymous_variant | Exon 8 of 8 | ENST00000345127.9 | NP_694571.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.320 AC: 48517AN: 151562Hom.: 8233 Cov.: 31
GnomAD3 exomes AF: 0.349 AC: 87749AN: 251368Hom.: 15874 AF XY: 0.348 AC XY: 47223AN XY: 135854
GnomAD4 exome AF: 0.360 AC: 526194AN: 1461700Hom.: 96623 Cov.: 47 AF XY: 0.358 AC XY: 260349AN XY: 727156
GnomAD4 genome AF: 0.320 AC: 48551AN: 151682Hom.: 8241 Cov.: 31 AF XY: 0.318 AC XY: 23558AN XY: 74110
ClinVar
Submissions by phenotype
not specified Benign:5
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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not provided Benign:3
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Epilepsy, progressive myoclonic, 1B Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at