chr6-41783574-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000359201(PRICKLE4):c.-545C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000359201 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRICKLE4 | ENST00000458694.6 | c.101C>T | p.Pro34Leu | missense_variant | Exon 3 of 8 | 5 | NM_013397.6 | ENSP00000404911.1 | ||
ENSG00000124593 | ENST00000335515.10 | n.101C>T | non_coding_transcript_exon_variant | Exon 2 of 9 | 2 | ENSP00000335185.6 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152016Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250524Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135432
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461552Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727046
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.101C>T (p.P34L) alteration is located in exon 3 (coding exon 1) of the PRICKLE4 gene. This alteration results from a C to T substitution at nucleotide position 101, causing the proline (P) at amino acid position 34 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at