rs922800521
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7
The NM_139058.3(ARX):c.825C>T(p.Ala275Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000504 in 1,190,442 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 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). Synonymous variant affecting the same amino acid position (i.e. A275A) has been classified as Likely benign.
Frequency
Consequence
NM_139058.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000889 AC: 1AN: 112540Hom.: 0 Cov.: 23 AF XY: 0.0000288 AC XY: 1AN XY: 34720
GnomAD3 exomes AF: 0.00000723 AC: 1AN: 138246Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 42662
GnomAD4 exome AF: 0.00000464 AC: 5AN: 1077902Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 349932
GnomAD4 genome AF: 0.00000889 AC: 1AN: 112540Hom.: 0 Cov.: 23 AF XY: 0.0000288 AC XY: 1AN XY: 34720
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis indicates that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge -
Intellectual disability, X-linked, with or without seizures, ARX-related;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at