chr22-24734100-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001255975.1(PIWIL3):c.1691G>T(p.Arg564Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,058 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001255975.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIWIL3 | NM_001255975.1 | c.1691G>T | p.Arg564Ile | missense_variant | 14/21 | ENST00000616349.5 | |
PIWIL3 | NM_001008496.3 | c.1691G>T | p.Arg564Ile | missense_variant | 14/21 | ||
PIWIL3 | NR_045648.1 | n.2322G>T | non_coding_transcript_exon_variant | 15/22 | |||
PIWIL3 | NR_045649.2 | n.2195G>T | non_coding_transcript_exon_variant | 15/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIWIL3 | ENST00000616349.5 | c.1691G>T | p.Arg564Ile | missense_variant | 14/21 | 1 | NM_001255975.1 | A2 | |
PIWIL3 | ENST00000332271.9 | c.1691G>T | p.Arg564Ile | missense_variant | 14/21 | 1 | P2 | ||
PIWIL3 | ENST00000527701.6 | c.*1663G>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/22 | 1 | ||||
PIWIL3 | ENST00000533313.6 | c.*1617G>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249590Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134834
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1459938Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726092
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.1691G>T (p.R564I) alteration is located in exon 14 (coding exon 13) of the PIWIL3 gene. This alteration results from a G to T substitution at nucleotide position 1691, causing the arginine (R) at amino acid position 564 to be replaced by an isoleucine (I). 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