rs75887545
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015338.6(ASXL1):āc.3498C>Gā(p.Ser1166Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,614,224 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
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.3498C>G | p.Ser1166Arg | missense_variant | 13/13 | ENST00000375687.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASXL1 | ENST00000375687.10 | c.3498C>G | p.Ser1166Arg | missense_variant | 13/13 | 5 | NM_015338.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00668 AC: 1017AN: 152222Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00178 AC: 446AN: 251262Hom.: 5 AF XY: 0.00141 AC XY: 191AN XY: 135808
GnomAD4 exome AF: 0.000668 AC: 976AN: 1461884Hom.: 10 Cov.: 31 AF XY: 0.000606 AC XY: 441AN XY: 727246
GnomAD4 genome ? AF: 0.00668 AC: 1017AN: 152340Hom.: 15 Cov.: 32 AF XY: 0.00669 AC XY: 498AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 16, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 04, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
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