rs797045300
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBS1BS2
The NM_139058.3(ARX):βc.441_464delβ(p.Ala148_Ala155del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000533 in 813,782 control chromosomes in the GnomAD database, including 2 homozygotes. There are 124 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (β β ). Synonymous variant affecting the same amino acid position (i.e. A147A) has been classified as Likely benign.
Frequency
Consequence
NM_139058.3 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARX | NM_139058.3 | c.441_464del | p.Ala148_Ala155del | inframe_deletion | 2/5 | ENST00000379044.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARX | ENST00000379044.5 | c.441_464del | p.Ala148_Ala155del | inframe_deletion | 2/5 | 1 | NM_139058.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000707 AC: 74AN: 104666Hom.: 0 Cov.: 21 AF XY: 0.000836 AC XY: 25AN XY: 29914
GnomAD3 exomes AF: 0.000393 AC: 1AN: 2544Hom.: 0 AF XY: 0.00314 AC XY: 1AN XY: 318
GnomAD4 exome AF: 0.000508 AC: 360AN: 709130Hom.: 2 AF XY: 0.000461 AC XY: 99AN XY: 214590
GnomAD4 genome AF: 0.000707 AC: 74AN: 104652Hom.: 0 Cov.: 21 AF XY: 0.000836 AC XY: 25AN XY: 29920
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 04, 2013 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | ARX: BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Intellectual disability, X-linked, with or without seizures, arx-related Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Jan 01, 2011 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
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 | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at