X-77682772-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_000489.6(ATRX):āc.2484G>Cā(p.Met828Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000364 in 1,208,612 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 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_000489.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.2484G>C | p.Met828Ile | missense_variant | 9/35 | ENST00000373344.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRX | ENST00000373344.11 | c.2484G>C | p.Met828Ile | missense_variant | 9/35 | 1 | NM_000489.6 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000360 AC: 4AN: 111078Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33316
GnomAD3 exomes AF: 0.0000384 AC: 7AN: 182127Hom.: 0 AF XY: 0.0000447 AC XY: 3AN XY: 67119
GnomAD4 exome AF: 0.0000364 AC: 40AN: 1097534Hom.: 0 Cov.: 34 AF XY: 0.0000386 AC XY: 14AN XY: 363006
GnomAD4 genome AF: 0.0000360 AC: 4AN: 111078Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33316
ClinVar
Submissions by phenotype
Alpha thalassemia-X-linked intellectual disability syndrome Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 25, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 20, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at