12-6934581-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_001940.4(ATN1):​c.279+3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000279 in 1,551,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 0 hom. )

Consequence

ATN1
NM_001940.4 splice_region, intron

Scores

2
Splicing: ADA: 0.001556
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.01
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 12-6934581-G-A is Benign according to our data. Variant chr12-6934581-G-A is described in ClinVar as [Benign]. Clinvar id is 3766688.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 191 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATN1NM_001940.4 linkc.279+3G>A splice_region_variant, intron_variant Intron 4 of 9 ENST00000396684.3 NP_001931.2 P54259

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATN1ENST00000396684.3 linkc.279+3G>A splice_region_variant, intron_variant Intron 4 of 9 1 NM_001940.4 ENSP00000379915.2 P54259
ATN1ENST00000356654.8 linkc.279+3G>A splice_region_variant, intron_variant Intron 4 of 9 1 ENSP00000349076.3 P54259

Frequencies

GnomAD3 genomes
AF:
0.00126
AC:
192
AN:
152184
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00432
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
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:
0.00
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000399
AC:
65
AN:
162934
Hom.:
0
AF XY:
0.000293
AC XY:
25
AN XY:
85468
show subpopulations
Gnomad AFR exome
AF:
0.00523
Gnomad AMR exome
AF:
0.000436
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000619
Gnomad OTH exome
AF:
0.000218
GnomAD4 exome
AF:
0.000173
AC:
242
AN:
1399660
Hom.:
0
Cov.:
29
AF XY:
0.000162
AC XY:
112
AN XY:
691194
show subpopulations
Gnomad4 AFR exome
AF:
0.00521
Gnomad4 AMR exome
AF:
0.000442
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000343
Gnomad4 OTH exome
AF:
0.000310
GnomAD4 genome
AF:
0.00125
AC:
191
AN:
152302
Hom.:
0
Cov.:
32
AF XY:
0.00138
AC XY:
103
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.00431
Gnomad4 AMR
AF:
0.000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.00109
Hom.:
0
Bravo
AF:
0.00134

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jun 28, 2024
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.37
CADD
Benign
14
DANN
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.0016
dbscSNV1_RF
Benign
0.15
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs148382908; hg19: chr12-7043744; API