rs145132837
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015338.6(ASXL1):āc.2957A>Gā(p.Asn986Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,614,144 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N986N) has been classified as Benign.
Frequency
Consequence
NM_015338.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASXL1 | NM_015338.6 | c.2957A>G | p.Asn986Ser | missense_variant | 13/13 | ENST00000375687.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASXL1 | ENST00000375687.10 | c.2957A>G | p.Asn986Ser | missense_variant | 13/13 | 5 | NM_015338.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00171 AC: 260AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00148 AC: 373AN: 251450Hom.: 1 AF XY: 0.00143 AC XY: 194AN XY: 135900
GnomAD4 exome AF: 0.00180 AC: 2631AN: 1461878Hom.: 8 Cov.: 30 AF XY: 0.00181 AC XY: 1317AN XY: 727248
GnomAD4 genome ? AF: 0.00171 AC: 261AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.00179 AC XY: 133AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 05, 2019 | This variant is associated with the following publications: (PMID: 29456859) - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | ASXL1: BP4, BS1, BS2 - |
ASXL1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 09, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Bohring-Opitz syndrome;C3463824:Myelodysplastic syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 10, 2021 | - - |
Bohring-Opitz syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at