chrX-25004688-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_139058.3(ARX):c.1671G>A(p.Thr557Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00406 in 1,164,057 control chromosomes in the GnomAD database, including 7 homozygotes. There are 1,540 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
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00332 AC: 376AN: 113263Hom.: 1 Cov.: 25 AF XY: 0.00356 AC XY: 126AN XY: 35419
GnomAD3 exomes AF: 0.00299 AC: 314AN: 105177Hom.: 0 AF XY: 0.00280 AC XY: 103AN XY: 36819
GnomAD4 exome AF: 0.00414 AC: 4345AN: 1050748Hom.: 6 Cov.: 31 AF XY: 0.00412 AC XY: 1414AN XY: 343046
GnomAD4 genome AF: 0.00332 AC: 376AN: 113309Hom.: 1 Cov.: 25 AF XY: 0.00355 AC XY: 126AN XY: 35475
ClinVar
Submissions by phenotype
not specified Benign:5
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Uncertain:1Benign:3
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Inborn genetic diseases Benign:1
This alteration is classified as 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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at