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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001940.4(ATN1):c.1473_1508del(p.Gln491_Gln502del) variant causes a inframe deletion change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q488Q) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000021 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000015 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ATN1
NM_001940.4 inframe_deletion
NM_001940.4 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.09
Genes affected
ATN1 (HGNC:3033): (atrophin 1) Dentatorubral pallidoluysian atrophy (DRPLA) is a rare neurodegenerative disorder characterized by cerebellar ataxia, myoclonic epilepsy, choreoathetosis, and dementia. The disorder is related to the expansion from 7-35 copies to 49-93 copies of a trinucleotide repeat (CAG/CAA) within this gene. The encoded protein includes a serine repeat and a region of alternating acidic and basic amino acids, as well as the variable glutamine repeat. Alternative splicing results in two transcripts variants that encode the same protein. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATN1 | NM_001940.4 | c.1473_1508del | p.Gln491_Gln502del | inframe_deletion | 5/10 | ENST00000396684.3 | |
ATN1 | NM_001007026.2 | c.1473_1508del | p.Gln491_Gln502del | inframe_deletion | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.1473_1508del | p.Gln491_Gln502del | inframe_deletion | 5/10 | 1 | NM_001940.4 | P1 | |
ATN1 | ENST00000356654.8 | c.1473_1508del | p.Gln491_Gln502del | inframe_deletion | 5/10 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000207 AC: 3AN: 145034Hom.: 0 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000153 AC: 22AN: 1438920Hom.: 0 AF XY: 0.0000153 AC XY: 11AN XY: 716734
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GnomAD4 genome AF: 0.0000207 AC: 3AN: 145134Hom.: 0 Cov.: 0 AF XY: 0.0000142 AC XY: 1AN XY: 70474
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at