rs144527582
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 1P and 18B. PP2BP4_ModerateBP6_Very_StrongBS1BS2
The NM_000489.6(ATRX):c.3641A>T(p.Asn1214Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000631 in 1,205,054 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N1214S) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.3641A>T | p.Asn1214Ile | missense_variant | 9/35 | ENST00000373344.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRX | ENST00000373344.11 | c.3641A>T | p.Asn1214Ile | missense_variant | 9/35 | 1 | NM_000489.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000341 AC: 38AN: 111459Hom.: 0 Cov.: 23 AF XY: 0.000267 AC XY: 9AN XY: 33679
GnomAD3 exomes AF: 0.000141 AC: 25AN: 177478Hom.: 0 AF XY: 0.0000955 AC XY: 6AN XY: 62802
GnomAD4 exome AF: 0.0000347 AC: 38AN: 1093538Hom.: 0 Cov.: 31 AF XY: 0.0000278 AC XY: 10AN XY: 359660
GnomAD4 genome ? AF: 0.000341 AC: 38AN: 111516Hom.: 0 Cov.: 23 AF XY: 0.000267 AC XY: 9AN XY: 33746
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 09, 2018 | - - |
Alpha thalassemia-X-linked intellectual disability syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at