rs398123423
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000489.6(ATRX):c.4374_4379delGGAGGA(p.Glu1459_Glu1460del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000498 in 1,204,437 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000489.6 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATRX | NM_000489.6 | c.4374_4379delGGAGGA | p.Glu1459_Glu1460del | disruptive_inframe_deletion | 15/35 | ENST00000373344.11 | NP_000480.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATRX | ENST00000373344.11 | c.4374_4379delGGAGGA | p.Glu1459_Glu1460del | disruptive_inframe_deletion | 15/35 | 1 | NM_000489.6 | ENSP00000362441.4 |
Frequencies
GnomAD3 genomes AF: 0.00000909 AC: 1AN: 110027Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32397
GnomAD3 exomes AF: 0.0000168 AC: 3AN: 178979Hom.: 0 AF XY: 0.0000308 AC XY: 2AN XY: 65011
GnomAD4 exome AF: 0.00000457 AC: 5AN: 1094410Hom.: 0 AF XY: 0.00000832 AC XY: 3AN XY: 360526
GnomAD4 genome AF: 0.00000909 AC: 1AN: 110027Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32397
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at