X-77682784-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2
The NM_000489.6(ATRX):c.2472G>C(p.Glu824Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000273 in 1,097,372 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E824Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_000489.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.2472G>C | p.Glu824Asp | missense_variant | Exon 9 of 35 | ENST00000373344.11 | NP_000480.3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.00000551 AC: 1AN: 181640Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66740
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097372Hom.: 0 Cov.: 34 AF XY: 0.00000551 AC XY: 2AN XY: 362848
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Alpha thalassemia-X-linked intellectual disability syndrome Uncertain:1Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at