chr20-32358849-A-AG
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_015338.6(ASXL1):c.57+23dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000096 in 1,270,438 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00036 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000061 ( 0 hom. )
Consequence
ASXL1
NM_015338.6 intron
NM_015338.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0760
Genes affected
ASXL1 (HGNC:18318): (ASXL transcriptional regulator 1) This gene is similar to the Drosophila additional sex combs gene, which encodes a chromatin-binding protein required for normal determination of segment identity in the developing embryo. The protein is a member of the Polycomb group of proteins, which are necessary for the maintenance of stable repression of homeotic and other loci. The protein is thought to disrupt chromatin in localized areas, enhancing transcription of certain genes while repressing the transcription of other genes. The protein encoded by this gene functions as a ligand-dependent co-activator for retinoic acid receptor in cooperation with nuclear receptor coactivator 1. Mutations in this gene are associated with myelodysplastic syndromes and chronic myelomonocytic leukemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 20-32358849-A-AG is Benign according to our data. Variant chr20-32358849-A-AG is described in ClinVar as [Benign]. Clinvar id is 1901363.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 54 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASXL1 | NM_015338.6 | c.57+23dup | intron_variant | ENST00000375687.10 | |||
ASXL1 | NM_001164603.1 | c.57+23dup | intron_variant | ||||
ASXL1 | XM_006723727.4 | c.57+23dup | intron_variant | ||||
ASXL1 | XM_047439945.1 | c.57+23dup | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASXL1 | ENST00000375687.10 | c.57+23dup | intron_variant | 5 | NM_015338.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000362 AC: 54AN: 149304Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000683 AC: 7AN: 102422Hom.: 0 AF XY: 0.0000528 AC XY: 3AN XY: 56796
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GnomAD4 exome AF: 0.0000607 AC: 68AN: 1121020Hom.: 0 Cov.: 33 AF XY: 0.0000590 AC XY: 33AN XY: 559552
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GnomAD4 genome ? AF: 0.000361 AC: 54AN: 149418Hom.: 0 Cov.: 31 AF XY: 0.000329 AC XY: 24AN XY: 72962
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at