chrX-77682038-C-G
Variant summary
Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_000489.6(ATRX):c.3218G>C(p.Ser1073Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000038 in 1,209,278 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1073S) has been classified as Likely benign.
Frequency
Consequence
NM_000489.6 missense
Scores
Clinical Significance
Conservation
Publications
- alpha thalassemia-X-linked intellectual disability syndromeInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics
- ATR-X-related syndromeInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- intellectual disability-hypotonic facies syndrome, X-linked, 1Inheritance: XL Classification: MODERATE Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.3218G>C | p.Ser1073Thr | missense_variant | Exon 9 of 35 | ENST00000373344.11 | NP_000480.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000538 AC: 6AN: 111593Hom.: 0 Cov.: 22 show subpopulations
GnomAD2 exomes AF: 0.000170 AC: 31AN: 182829 AF XY: 0.000133 show subpopulations
GnomAD4 exome AF: 0.0000364 AC: 40AN: 1097685Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 13AN XY: 363153 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000538 AC: 6AN: 111593Hom.: 0 Cov.: 22 AF XY: 0.0000296 AC XY: 1AN XY: 33789 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Alpha thalassemia-X-linked intellectual disability syndrome Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at