rs1313243538
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_139058.3(ARX):c.351C>A(p.Ala117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000289 in 761,271 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000019 ( 0 hom., 1 hem., cov: 22)
Exomes 𝑓: 0.000031 ( 0 hom. 8 hem. )
Consequence
ARX
NM_139058.3 synonymous
NM_139058.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.789
Genes affected
ARX (HGNC:18060): (aristaless related homeobox) This gene is a homeobox-containing gene expressed during development. The expressed protein contains two conserved domains, a C-peptide (or aristaless domain) and the prd-like class homeobox domain. It is a member of the group-II aristaless-related protein family whose members are expressed primarily in the central and/or peripheral nervous system. This gene is thought to be involved in CNS development. Expansion of a polyalanine tract and other mutations in this gene cause X-linked cognitive disability and epilepsy. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant X-25013644-G-T is Benign according to our data. Variant chrX-25013644-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 540223.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.789 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome4 at 8 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARX | NM_139058.3 | c.351C>A | p.Ala117= | synonymous_variant | 2/5 | ENST00000379044.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARX | ENST00000379044.5 | c.351C>A | p.Ala117= | synonymous_variant | 2/5 | 1 | NM_139058.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000188 AC: 2AN: 106647Hom.: 0 Cov.: 22 AF XY: 0.0000316 AC XY: 1AN XY: 31639
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GnomAD4 exome AF: 0.0000306 AC: 20AN: 654624Hom.: 0 Cov.: 31 AF XY: 0.0000402 AC XY: 8AN XY: 198926
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GnomAD4 genome ? AF: 0.0000188 AC: 2AN: 106647Hom.: 0 Cov.: 22 AF XY: 0.0000316 AC XY: 1AN XY: 31651
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual disability, X-linked, with or without seizures, arx-related;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at