rs199780997
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_000489.6(ATRX):āc.1041T>Gā(p.Ile347Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000909 in 1,209,835 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 32 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I347V) 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.1041T>G | p.Ile347Met | missense_variant | 9/35 | ENST00000373344.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRX | ENST00000373344.11 | c.1041T>G | p.Ile347Met | missense_variant | 9/35 | 1 | NM_000489.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000446 AC: 5AN: 112224Hom.: 0 Cov.: 24 AF XY: 0.0000581 AC XY: 2AN XY: 34402
GnomAD3 exomes AF: 0.0000549 AC: 10AN: 182128Hom.: 0 AF XY: 0.0000299 AC XY: 2AN XY: 66952
GnomAD4 exome AF: 0.0000957 AC: 105AN: 1097557Hom.: 0 Cov.: 32 AF XY: 0.0000826 AC XY: 30AN XY: 363009
GnomAD4 genome ? AF: 0.0000445 AC: 5AN: 112278Hom.: 0 Cov.: 24 AF XY: 0.0000580 AC XY: 2AN XY: 34466
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Alpha thalassemia-X-linked intellectual disability syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at