chr22-24734113-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001255975.1(PIWIL3):c.1678C>T(p.Arg560Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,612,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIWIL3 | NM_001255975.1 | c.1678C>T | p.Arg560Trp | missense_variant | 14/21 | ENST00000616349.5 | |
PIWIL3 | NM_001008496.3 | c.1678C>T | p.Arg560Trp | missense_variant | 14/21 | ||
PIWIL3 | NR_045648.1 | n.2309C>T | non_coding_transcript_exon_variant | 15/22 | |||
PIWIL3 | NR_045649.2 | n.2182C>T | non_coding_transcript_exon_variant | 15/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIWIL3 | ENST00000616349.5 | c.1678C>T | p.Arg560Trp | missense_variant | 14/21 | 1 | NM_001255975.1 | A2 | |
PIWIL3 | ENST00000332271.9 | c.1678C>T | p.Arg560Trp | missense_variant | 14/21 | 1 | P2 | ||
PIWIL3 | ENST00000527701.6 | c.*1650C>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/22 | 1 | ||||
PIWIL3 | ENST00000533313.6 | c.*1604C>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249728Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134910
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460182Hom.: 0 Cov.: 30 AF XY: 0.00000964 AC XY: 7AN XY: 726252
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74414
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2023 | The c.1678C>T (p.R560W) alteration is located in exon 14 (coding exon 13) of the PIWIL3 gene. This alteration results from a C to T substitution at nucleotide position 1678, causing the arginine (R) at amino acid position 560 to be replaced by a tryptophan (W). 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