chr22-24719788-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001255975.1(PIWIL3):c.2465G>A(p.Arg822His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,074 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R822C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001255975.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIWIL3 | NM_001255975.1 | c.2465G>A | p.Arg822His | missense_variant | 20/21 | ENST00000616349.5 | |
PIWIL3 | NM_001008496.3 | c.2492G>A | p.Arg831His | missense_variant | 20/21 | ||
PIWIL3 | NR_045648.1 | n.3096G>A | non_coding_transcript_exon_variant | 21/22 | |||
PIWIL3 | NR_045649.2 | n.2969G>A | non_coding_transcript_exon_variant | 21/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIWIL3 | ENST00000616349.5 | c.2465G>A | p.Arg822His | missense_variant | 20/21 | 1 | NM_001255975.1 | A2 | |
PIWIL3 | ENST00000332271.9 | c.2492G>A | p.Arg831His | missense_variant | 20/21 | 1 | P2 | ||
PIWIL3 | ENST00000527701.6 | c.*2437G>A | 3_prime_UTR_variant, NMD_transcript_variant | 21/22 | 1 | ||||
PIWIL3 | ENST00000533313.6 | c.*2391G>A | 3_prime_UTR_variant, NMD_transcript_variant | 21/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251412Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135884
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460986Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726882
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.2492G>A (p.R831H) alteration is located in exon 20 (coding exon 19) of the PIWIL3 gene. This alteration results from a G to A substitution at nucleotide position 2492, causing the arginine (R) at amino acid position 831 to be replaced by a histidine (H). 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