rs201776257
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_030632.3(ASXL3):c.2342C>T(p.Pro781Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0003 in 1,613,658 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_030632.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASXL3 | NM_030632.3 | c.2342C>T | p.Pro781Leu | missense_variant | 11/12 | ENST00000269197.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASXL3 | ENST00000269197.12 | c.2342C>T | p.Pro781Leu | missense_variant | 11/12 | 5 | NM_030632.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000230 AC: 57AN: 248176Hom.: 0 AF XY: 0.000282 AC XY: 38AN XY: 134772
GnomAD4 exome AF: 0.000300 AC: 438AN: 1461514Hom.: 0 Cov.: 33 AF XY: 0.000305 AC XY: 222AN XY: 727038
GnomAD4 genome ? AF: 0.000302 AC: 46AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 26, 2015 | - - |
ASXL3-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 08, 2023 | The ASXL3 c.2342C>T variant is predicted to result in the amino acid substitution p.Pro781Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.037% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Although we suspect this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 08, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at