GeneBe

rs60216939

Positions:

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.09
Variant links:
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
ATN1NM_001940.4 linkuse as main transcriptc.1473_1508del p.Gln491_Gln502del inframe_deletion 5/10 ENST00000396684.3
ATN1NM_001007026.2 linkuse as main transcriptc.1473_1508del p.Gln491_Gln502del inframe_deletion 5/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATN1ENST00000396684.3 linkuse as main transcriptc.1473_1508del p.Gln491_Gln502del inframe_deletion 5/101 NM_001940.4 P1
ATN1ENST00000356654.8 linkuse as main transcriptc.1473_1508del p.Gln491_Gln502del inframe_deletion 5/101 P1

Frequencies

GnomAD3 genomes
AF:
0.0000207
AC:
3
AN:
145034
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000517
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000150
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000153
AC:
22
AN:
1438920
Hom.:
0
AF XY:
0.0000153
AC XY:
11
AN XY:
716734
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000249
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000173
Gnomad4 OTH exome
AF:
0.0000168
GnomAD4 genome
AF:
0.0000207
AC:
3
AN:
145134
Hom.:
0
Cov.:
0
AF XY:
0.0000142
AC XY:
1
AN XY:
70474
show subpopulations
Gnomad4 AFR
AF:
0.0000516
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000150
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs60216939; hg19: chr12-7045891; API