rs1006404746
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_139058.3(ARX):c.663C>T(p.Thr221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000374 in 1,150,184 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T221T) has been classified as Likely benign.
Frequency
Consequence
NM_139058.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARX | NM_139058.3 | c.663C>T | p.Thr221= | synonymous_variant | 2/5 | ENST00000379044.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARX | ENST00000379044.5 | c.663C>T | p.Thr221= | synonymous_variant | 2/5 | 1 | NM_139058.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 16AN: 110346Hom.: 0 Cov.: 23 AF XY: 0.0000610 AC XY: 2AN XY: 32780
GnomAD3 exomes AF: 0.0000533 AC: 5AN: 93801Hom.: 0 AF XY: 0.0000609 AC XY: 2AN XY: 32865
GnomAD4 exome AF: 0.0000260 AC: 27AN: 1039838Hom.: 0 Cov.: 32 AF XY: 0.0000177 AC XY: 6AN XY: 339242
GnomAD4 genome ? AF: 0.000145 AC: 16AN: 110346Hom.: 0 Cov.: 23 AF XY: 0.0000610 AC XY: 2AN XY: 32780
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2020 | - - |
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 | Invitae | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at