22-24719489-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001255975.1(PIWIL3):c.2605C>T(p.Arg869Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00406 in 1,589,020 control chromosomes in the GnomAD database, including 247 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001255975.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIWIL3 | NM_001255975.1 | c.2605C>T | p.Arg869Cys | missense_variant | 21/21 | ENST00000616349.5 | |
PIWIL3 | NM_001008496.3 | c.2632C>T | p.Arg878Cys | missense_variant | 21/21 | ||
PIWIL3 | NR_045648.1 | n.3236C>T | non_coding_transcript_exon_variant | 22/22 | |||
PIWIL3 | NR_045649.2 | n.3109C>T | non_coding_transcript_exon_variant | 22/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIWIL3 | ENST00000616349.5 | c.2605C>T | p.Arg869Cys | missense_variant | 21/21 | 1 | NM_001255975.1 | A2 | |
PIWIL3 | ENST00000332271.9 | c.2632C>T | p.Arg878Cys | missense_variant | 21/21 | 1 | P2 | ||
PIWIL3 | ENST00000527701.6 | c.*2577C>T | 3_prime_UTR_variant, NMD_transcript_variant | 22/22 | 1 | ||||
PIWIL3 | ENST00000533313.6 | c.*2531C>T | 3_prime_UTR_variant, NMD_transcript_variant | 22/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0216 AC: 3286AN: 152172Hom.: 119 Cov.: 32
GnomAD3 exomes AF: 0.00613 AC: 1410AN: 230202Hom.: 56 AF XY: 0.00434 AC XY: 539AN XY: 124242
GnomAD4 exome AF: 0.00220 AC: 3158AN: 1436730Hom.: 128 Cov.: 30 AF XY: 0.00196 AC XY: 1397AN XY: 713302
GnomAD4 genome ? AF: 0.0216 AC: 3290AN: 152290Hom.: 119 Cov.: 32 AF XY: 0.0210 AC XY: 1564AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at