3-63912684-GGCAGCAGCAGCAGCAGCAGCA-GGCAGCAGCAGCAGCA
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_001377405.1(ATXN7):c.113_118delAGCAGC(p.Gln38_Gln39del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00125 in 1,087,052 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0015 ( 0 hom., cov: 23)
Exomes 𝑓: 0.0012 ( 0 hom. )
Consequence
ATXN7
NM_001377405.1 disruptive_inframe_deletion
NM_001377405.1 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.84
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001377405.1
BS2
High AC in GnomAd4 at 218 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN7 | NM_001377405.1 | c.113_118delAGCAGC | p.Gln38_Gln39del | disruptive_inframe_deletion | 3/13 | ENST00000674280.1 | NP_001364334.1 | |
ATXN7 | NM_001177387.1 | c.113_118delAGCAGC | p.Gln38_Gln39del | disruptive_inframe_deletion | 2/13 | NP_001170858.1 | ||
ATXN7 | NM_000333.4 | c.113_118delAGCAGC | p.Gln38_Gln39del | disruptive_inframe_deletion | 3/13 | NP_000324.1 | ||
ATXN7 | NM_001377406.1 | c.113_118delAGCAGC | p.Gln38_Gln39del | disruptive_inframe_deletion | 2/12 | NP_001364335.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN7 | ENST00000674280.1 | c.113_118delAGCAGC | p.Gln38_Gln39del | disruptive_inframe_deletion | 3/13 | NM_001377405.1 | ENSP00000501377.1 |
Frequencies
GnomAD3 genomes AF: 0.00150 AC: 217AN: 144616Hom.: 0 Cov.: 23
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GnomAD4 exome AF: 0.00121 AC: 1140AN: 942334Hom.: 0 AF XY: 0.00121 AC XY: 539AN XY: 446524
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GnomAD4 genome AF: 0.00151 AC: 218AN: 144718Hom.: 0 Cov.: 23 AF XY: 0.00126 AC XY: 89AN XY: 70412
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at