chrX-49175812-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006150.5(PRICKLE3):c.1709T>A(p.Leu570Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,210,844 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006150.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRICKLE3 | NM_006150.5 | c.1709T>A | p.Leu570Gln | missense_variant | 9/9 | ENST00000599218.6 | |
PRICKLE3 | NM_001307979.2 | c.1505T>A | p.Leu502Gln | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRICKLE3 | ENST00000599218.6 | c.1709T>A | p.Leu570Gln | missense_variant | 9/9 | 1 | NM_006150.5 | P3 | |
PRICKLE3 | ENST00000453382.5 | c.1505T>A | p.Leu502Gln | missense_variant | 8/8 | 5 | A2 | ||
PRICKLE3 | ENST00000540849.5 | c.*1171T>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000888 AC: 1AN: 112661Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34813
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183436Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67872
GnomAD4 exome AF: 0.00000728 AC: 8AN: 1098183Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 8AN XY: 363539
GnomAD4 genome AF: 0.00000888 AC: 1AN: 112661Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34813
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at