rs374244026
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_000489.6(ATRX):c.6871A>G(p.Ile2291Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,208,846 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I2291M) has been classified as Benign.
Frequency
Consequence
NM_000489.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.6871A>G | p.Ile2291Val | missense_variant | 32/35 | ENST00000373344.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRX | ENST00000373344.11 | c.6871A>G | p.Ile2291Val | missense_variant | 32/35 | 1 | NM_000489.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000896 AC: 10AN: 111585Hom.: 0 Cov.: 22 AF XY: 0.000118 AC XY: 4AN XY: 33791
GnomAD3 exomes AF: 0.0000437 AC: 8AN: 183204Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67766
GnomAD4 exome AF: 0.0000456 AC: 50AN: 1097261Hom.: 0 Cov.: 30 AF XY: 0.0000386 AC XY: 14AN XY: 362919
GnomAD4 genome ? AF: 0.0000896 AC: 10AN: 111585Hom.: 0 Cov.: 22 AF XY: 0.000118 AC XY: 4AN XY: 33791
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 07, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Alpha thalassemia-X-linked intellectual disability syndrome Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 08, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at