2-25742222-G-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_018263.6(ASXL2):c.4115C>T(p.Ala1372Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1372G) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Consequence
ASXL2
NM_018263.6 missense
NM_018263.6 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 5.99
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.24056637).
BP6
Variant 2-25742222-G-A is Benign according to our data. Variant chr2-25742222-G-A is described in ClinVar as [Benign]. Clinvar id is 1354065.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ASXL2 | NM_018263.6 | c.4115C>T | p.Ala1372Val | missense_variant | Exon 13 of 13 | ENST00000435504.9 | NP_060733.4 | |
| ASXL2 | NM_001369346.1 | c.3941C>T | p.Ala1314Val | missense_variant | Exon 11 of 11 | NP_001356275.1 | ||
| ASXL2 | NM_001369347.1 | c.3335C>T | p.Ala1112Val | missense_variant | Exon 10 of 10 | NP_001356276.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ASXL2 | ENST00000435504.9 | c.4115C>T | p.Ala1372Val | missense_variant | Exon 13 of 13 | 5 | NM_018263.6 | ENSP00000391447.3 | ||
| ASXL2 | ENST00000336112.9 | c.4112C>T | p.Ala1371Val | missense_variant | Exon 12 of 12 | 1 | ENSP00000337250.5 | |||
| ASXL2 | ENST00000404843.5 | c.2564C>T | p.Ala855Val | missense_variant | Exon 10 of 10 | 1 | ENSP00000383920.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 24, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;T;T
Polyphen
D;.;D
Vest4
MutPred
Loss of glycosylation at S1376 (P = 0.1255);.;.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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
Publications
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