X-77508429-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_000489.6(ATRX):c.7401G>A(p.Met2467Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000298 in 1,208,118 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 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. M2467T) has been classified as Likely benign.
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.7401G>A | p.Met2467Ile | missense_variant | 35/35 | ENST00000373344.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRX | ENST00000373344.11 | c.7401G>A | p.Met2467Ile | missense_variant | 35/35 | 1 | NM_000489.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000894 AC: 1AN: 111854Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 34010
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183364Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67846
GnomAD4 exome AF: 0.0000319 AC: 35AN: 1096264Hom.: 0 Cov.: 31 AF XY: 0.0000221 AC XY: 8AN XY: 361768
GnomAD4 genome ? AF: 0.00000894 AC: 1AN: 111854Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 34010
ClinVar
Submissions by phenotype
Alpha thalassemia-X-linked intellectual disability syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at