rs797045294
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_139058.3(ARX):c.300G>A(p.Ala100=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000472 in 888,972 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_139058.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARX | NM_139058.3 | c.300G>A | p.Ala100= | synonymous_variant | 2/5 | ENST00000379044.5 | NP_620689.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARX | ENST00000379044.5 | c.300G>A | p.Ala100= | synonymous_variant | 2/5 | 1 | NM_139058.3 | ENSP00000368332 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000367 AC: 4AN: 109067Hom.: 0 Cov.: 23 AF XY: 0.0000611 AC XY: 2AN XY: 32745
GnomAD4 exome AF: 0.0000487 AC: 38AN: 779905Hom.: 0 Cov.: 32 AF XY: 0.0000681 AC XY: 16AN XY: 234939
GnomAD4 genome AF: 0.0000367 AC: 4AN: 109067Hom.: 0 Cov.: 23 AF XY: 0.0000611 AC XY: 2AN XY: 32745
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 14, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 30, 2020 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 18, 2014 | - - |
Intellectual disability, X-linked, with or without seizures, arx-related;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at