3-63912684-G-GGCAGCAGCA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP3BS1_SupportingBS2

The NM_001377405.1(ATXN7):​c.110_118dupAGCAGCAGC​(p.Gln37_Gln39dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.046 in 1,086,962 control chromosomes in the GnomAD database, including 796 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.034 ( 92 hom., cov: 23)
Exomes 𝑓: 0.048 ( 704 hom. )

Consequence

ATXN7
NM_001377405.1 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity no assertion criteria provided U:1B:1

Conservation

PhyloP100: 4.10
Variant links:
Genes affected
ATXN7 (HGNC:10560): (ataxin 7) The autosomal dominant cerebellar ataxias (ADCA) are a heterogeneous group of neurodegenerative disorders characterized by progressive degeneration of the cerebellum, brain stem and spinal cord. Clinically, ADCA has been divided into three groups: ADCA types I-III. ADCAI is genetically heterogeneous, with five genetic loci, designated spinocerebellar ataxia (SCA) 1, 2, 3, 4 and 6, being assigned to five different chromosomes. ADCAII, which always presents with retinal degeneration (SCA7), and ADCAIII often referred to as the 'pure' cerebellar syndrome (SCA5), are most likely homogeneous disorders. Several SCA genes have been cloned and shown to contain CAG repeats in their coding regions. ADCA is caused by the expansion of the CAG repeats, producing an elongated polyglutamine tract in the corresponding protein. The expanded repeats are variable in size and unstable, usually increasing in size when transmitted to successive generations. This locus has been mapped to chromosome 3, and it has been determined that the diseased allele associated with spinocerebellar ataxia-7 contains 37-306 CAG repeats (near the N-terminus), compared to 4-35 in the normal allele. The encoded protein is a component of the SPT3/TAF9/GCN5 acetyltransferase (STAGA) and TBP-free TAF-containing (TFTC) chromatin remodeling complexes, and it thus plays a role in transcriptional regulation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001377405.1
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0342 (4953/144692) while in subpopulation NFE AF= 0.0483 (3159/65426). AF 95% confidence interval is 0.0469. There are 92 homozygotes in gnomad4. There are 2376 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 4953 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATXN7NM_001377405.1 linkc.110_118dupAGCAGCAGC p.Gln37_Gln39dup disruptive_inframe_insertion 3/13 ENST00000674280.1 NP_001364334.1
ATXN7NM_001177387.1 linkc.110_118dupAGCAGCAGC p.Gln37_Gln39dup disruptive_inframe_insertion 2/13 NP_001170858.1 O15265-2
ATXN7NM_000333.4 linkc.110_118dupAGCAGCAGC p.Gln37_Gln39dup disruptive_inframe_insertion 3/13 NP_000324.1 O15265-1Q9UPD8
ATXN7NM_001377406.1 linkc.110_118dupAGCAGCAGC p.Gln37_Gln39dup disruptive_inframe_insertion 2/12 NP_001364335.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATXN7ENST00000674280.1 linkc.110_118dupAGCAGCAGC p.Gln37_Gln39dup disruptive_inframe_insertion 3/13 NM_001377405.1 ENSP00000501377.1 O15265-1

Frequencies

GnomAD3 genomes
AF:
0.0342
AC:
4952
AN:
144590
Hom.:
93
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.0134
Gnomad AMI
AF:
0.0618
Gnomad AMR
AF:
0.0341
Gnomad ASJ
AF:
0.0528
Gnomad EAS
AF:
0.00649
Gnomad SAS
AF:
0.0227
Gnomad FIN
AF:
0.0356
Gnomad MID
AF:
0.0296
Gnomad NFE
AF:
0.0483
Gnomad OTH
AF:
0.0369
GnomAD3 exomes
AF:
0.0215
AC:
223
AN:
10356
Hom.:
4
AF XY:
0.0226
AC XY:
125
AN XY:
5542
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00698
Gnomad ASJ exome
AF:
0.0116
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00681
Gnomad FIN exome
AF:
0.0237
Gnomad NFE exome
AF:
0.0290
Gnomad OTH exome
AF:
0.0150
GnomAD4 exome
AF:
0.0478
AC:
45017
AN:
942270
Hom.:
704
Cov.:
26
AF XY:
0.0474
AC XY:
21160
AN XY:
446526
show subpopulations
Gnomad4 AFR exome
AF:
0.0103
Gnomad4 AMR exome
AF:
0.0349
Gnomad4 ASJ exome
AF:
0.0596
Gnomad4 EAS exome
AF:
0.00655
Gnomad4 SAS exome
AF:
0.0310
Gnomad4 FIN exome
AF:
0.0277
Gnomad4 NFE exome
AF:
0.0502
Gnomad4 OTH exome
AF:
0.0410
GnomAD4 genome
AF:
0.0342
AC:
4953
AN:
144692
Hom.:
92
Cov.:
23
AF XY:
0.0338
AC XY:
2376
AN XY:
70390
show subpopulations
Gnomad4 AFR
AF:
0.0133
Gnomad4 AMR
AF:
0.0340
Gnomad4 ASJ
AF:
0.0528
Gnomad4 EAS
AF:
0.00650
Gnomad4 SAS
AF:
0.0236
Gnomad4 FIN
AF:
0.0356
Gnomad4 NFE
AF:
0.0483
Gnomad4 OTH
AF:
0.0365

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Retinal dystrophy Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingInstitute of Human Genetics, Univ. Regensburg, Univ. RegensburgJan 01, 2022- -
ATXN7-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJul 03, 2020This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

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: rs193922929; hg19: chr3-63898360; API