chrX-77654205-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_000489.6(ATRX):c.4215-5G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,185,355 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 58 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000489.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.4215-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000373344.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATRX | ENST00000373344.11 | c.4215-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000489.6 | P3 | |||
ATRX | ENST00000395603.7 | c.4101-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
ATRX | ENST00000624166.3 | c.4011-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
ATRX | ENST00000480283.5 | c.*3843-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000170 AC: 19AN: 111550Hom.: 0 Cov.: 23 AF XY: 0.000148 AC XY: 5AN XY: 33878
GnomAD3 exomes AF: 0.000143 AC: 26AN: 181292Hom.: 0 AF XY: 0.000181 AC XY: 12AN XY: 66390
GnomAD4 exome AF: 0.000157 AC: 169AN: 1073753Hom.: 0 Cov.: 26 AF XY: 0.000155 AC XY: 53AN XY: 341085
GnomAD4 genome AF: 0.000179 AC: 20AN: 111602Hom.: 0 Cov.: 23 AF XY: 0.000147 AC XY: 5AN XY: 33940
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 18, 2018 | This alteration is classified as 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 17, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 23, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at