rs542568224
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1BS2_Supporting
The NM_015338.6(ASXL1):c.3635C>T(p.Ser1212Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,613,820 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_015338.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000337 AC: 84AN: 249404Hom.: 1 AF XY: 0.000422 AC XY: 57AN XY: 135060
GnomAD4 exome AF: 0.000143 AC: 209AN: 1461490Hom.: 3 Cov.: 31 AF XY: 0.000194 AC XY: 141AN XY: 727034
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74490
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 06, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | ASXL1: BP4, BS1 - |
Uncertain significance, criteria provided, single submitter | research | Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre | Mar 08, 2024 | The variant is now downgraded to VUS based on updated frequency (PMID: 31130284) - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 19, 2020 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at