rs886041066
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_018263.6(ASXL2):c.2081_2082insG(p.Gly696ArgfsTer11) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
ASXL2
NM_018263.6 frameshift
NM_018263.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.43
Genes affected
ASXL2 (HGNC:23805): (ASXL transcriptional regulator 2) This gene encodes a member of a family of epigenetic regulators that bind various histone-modifying enzymes and are involved in the assembly of transcription factors at specific genomic loci. Naturally occurring mutations in this gene are associated with cancer in several tissue types (breast, bladder, pancreas, ovary, prostate, and blood). This gene plays an important role in neurodevelopment, cardiac function, adipogenesis, and osteoclastogenesis. [provided by RefSeq, Feb 2017]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 5 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 2-25744255-G-GC is Pathogenic according to our data. Variant chr2-25744255-G-GC is described in ClinVar as [Pathogenic]. Clinvar id is 268123.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASXL2 | NM_018263.6 | c.2081_2082insG | p.Gly696ArgfsTer11 | frameshift_variant | 13/13 | ENST00000435504.9 | |
ASXL2 | NM_001369346.1 | c.1907_1908insG | p.Gly638ArgfsTer11 | frameshift_variant | 11/11 | ||
ASXL2 | NM_001369347.1 | c.1301_1302insG | p.Gly436ArgfsTer11 | frameshift_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASXL2 | ENST00000435504.9 | c.2081_2082insG | p.Gly696ArgfsTer11 | frameshift_variant | 13/13 | 5 | NM_018263.6 | P4 | |
ASXL2 | ENST00000336112.9 | c.2078_2079insG | p.Gly695ArgfsTer11 | frameshift_variant | 12/12 | 1 | A2 | ||
ASXL2 | ENST00000404843.5 | c.1301_1302insG | p.Gly436ArgfsTer11 | frameshift_variant | 9/10 | 1 | A2 | ||
ASXL2 | ENST00000673455.1 | c.1301_1302insG | p.Gly436ArgfsTer11 | frameshift_variant | 10/10 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Shashi-Pena syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 11, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at