rs3746609
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015338.6(ASXL1):c.1954G>A(p.Gly652Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00672 in 1,602,238 control chromosomes in the GnomAD database, including 401 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G652G) 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.1954G>A | p.Gly652Ser | missense_variant | 13/13 | ENST00000375687.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASXL1 | ENST00000375687.10 | c.1954G>A | p.Gly652Ser | missense_variant | 13/13 | 5 | NM_015338.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00870 AC: 1323AN: 152112Hom.: 32 Cov.: 32
GnomAD3 exomes AF: 0.0191 AC: 4317AN: 225642Hom.: 173 AF XY: 0.0155 AC XY: 1931AN XY: 124220
GnomAD4 exome AF: 0.00651 AC: 9435AN: 1450008Hom.: 366 Cov.: 30 AF XY: 0.00608 AC XY: 4382AN XY: 720604
GnomAD4 genome ? AF: 0.00874 AC: 1330AN: 152230Hom.: 35 Cov.: 32 AF XY: 0.00956 AC XY: 712AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2018 | - - |
not specified Benign:2Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 06, 2015 | - - |
Bohring-Opitz syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at