chrX-77697597-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_000489.6(ATRX):c.228G>A(p.Ser76Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00513 in 1,208,385 control chromosomes in the GnomAD database, including 233 homozygotes. There are 1,550 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000489.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.228G>A | p.Ser76Ser | synonymous_variant | Exon 4 of 35 | ENST00000373344.11 | NP_000480.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0276 AC: 3081AN: 111502Hom.: 109 Cov.: 23 AF XY: 0.0232 AC XY: 783AN XY: 33742
GnomAD3 exomes AF: 0.00780 AC: 1425AN: 182592Hom.: 55 AF XY: 0.00425 AC XY: 285AN XY: 67122
GnomAD4 exome AF: 0.00284 AC: 3113AN: 1096829Hom.: 124 Cov.: 29 AF XY: 0.00211 AC XY: 765AN XY: 362371
GnomAD4 genome AF: 0.0277 AC: 3086AN: 111556Hom.: 109 Cov.: 23 AF XY: 0.0232 AC XY: 785AN XY: 33806
ClinVar
Submissions by phenotype
not specified Benign:5
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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Alpha thalassemia-X-linked intellectual disability syndrome Benign:2
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not provided Benign:2
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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. -
Acquired hemoglobin H disease;C1845055:Alpha thalassemia-X-linked intellectual disability syndrome;C4759781:Intellectual disability-hypotonic facies syndrome, X-linked, 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at