chr12-6936728-ACAGCAGCAGCAGCAGCAGCAGCAG-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001940.4(ATN1):c.1485_1508del(p.Gln495_Gln502del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00152 in 1,581,842 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. Q488Q) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0016 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0015 ( 14 hom. )
Consequence
ATN1
NM_001940.4 inframe_deletion
NM_001940.4 inframe_deletion
Scores
Not classified
Clinical Significance
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 12-6936728-ACAGCAGCAGCAGCAGCAGCAGCAG-A is Benign according to our data. Variant chr12-6936728-ACAGCAGCAGCAGCAGCAGCAGCAG-A is described in ClinVar as [Benign]. Clinvar id is 2642646.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 225 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATN1 | NM_001940.4 | c.1485_1508del | p.Gln495_Gln502del | inframe_deletion | 5/10 | ENST00000396684.3 | |
ATN1 | NM_001007026.2 | c.1485_1508del | p.Gln495_Gln502del | inframe_deletion | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.1485_1508del | p.Gln495_Gln502del | inframe_deletion | 5/10 | 1 | NM_001940.4 | P1 | |
ATN1 | ENST00000356654.8 | c.1485_1508del | p.Gln495_Gln502del | inframe_deletion | 5/10 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00155 AC: 225AN: 145032Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00152 AC: 2180AN: 1436710Hom.: 14 AF XY: 0.00160 AC XY: 1146AN XY: 715582
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GnomAD4 genome ? AF: 0.00156 AC: 226AN: 145132Hom.: 0 Cov.: 0 AF XY: 0.00167 AC XY: 118AN XY: 70474
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | ATN1: BS1, BS2 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at