chr12-6936728-ACAGCAGCAGCAGCAGCAG-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_001940.4(ATN1):c.1491_1508del(p.Gln497_Gln502del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00693 in 1,578,214 control chromosomes in the GnomAD database, including 266 homozygotes. Variant has been reported in Lovd as Likely benign (no stars). Synonymous variant affecting the same amino acid position (i.e. Q488Q) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.024 ( 136 hom., cov: 0)
Exomes 𝑓: 0.0052 ( 130 hom. )
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
?
Variant 12-6936728-ACAGCAGCAGCAGCAGCAG-A is Benign according to our data. Variant chr12-6936728-ACAGCAGCAGCAGCAGCAG-A is described in Lovd as [Likely_benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0761 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATN1 | NM_001940.4 | c.1491_1508del | p.Gln497_Gln502del | inframe_deletion | 5/10 | ENST00000396684.3 | |
ATN1 | NM_001007026.2 | c.1491_1508del | p.Gln497_Gln502del | inframe_deletion | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATN1 | ENST00000396684.3 | c.1491_1508del | p.Gln497_Gln502del | inframe_deletion | 5/10 | 1 | NM_001940.4 | P1 | |
ATN1 | ENST00000356654.8 | c.1491_1508del | p.Gln497_Gln502del | inframe_deletion | 5/10 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0239 AC: 3462AN: 145000Hom.: 135 Cov.: 0
GnomAD3 genomes
?
AF:
AC:
3462
AN:
145000
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00521 AC: 7472AN: 1433114Hom.: 130 AF XY: 0.00520 AC XY: 3713AN XY: 713844
GnomAD4 exome
AF:
AC:
7472
AN:
1433114
Hom.:
AF XY:
AC XY:
3713
AN XY:
713844
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0239 AC: 3469AN: 145100Hom.: 136 Cov.: 0 AF XY: 0.0240 AC XY: 1689AN XY: 70456
GnomAD4 genome
?
AF:
AC:
3469
AN:
145100
Hom.:
Cov.:
0
AF XY:
AC XY:
1689
AN XY:
70456
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at