3-63912684-GGCAGCAGCAGCAGCAGCAGCA-GGCAGCAGCA

Variant names:

• chr3-63912684-GGCAGCAGCAGCA-G
• rs193922929
• NM_001377405.1:c.107_118delAGCAGCAGCAGC

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3 BS2

The NM_001377405.1(ATXN7):​c.107_118delAGCAGCAGCAGC​(p.Gln36_Gln39del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000167 in 1,087,036 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00024 (0 hom., cov: 23)
  • Exomes 𝑓: 0.00015 (0 hom.)
• Consequence: ATXN7 NM_001377405.1 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.84
• Publications: 0 publications found

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]

ATXN7 Gene-Disease associations (from GenCC):

• spinocerebellar ataxia 7

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• spinocerebellar ataxia type 7

  Inheritance: AD Classification: MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001377405.1
• BS2: High AC in GnomAd4 at 35 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377405.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7	NM_001377405.1	MANE Select	c.107_118delAGCAGCAGCAGC	p.Gln36_Gln39del	disruptive_inframe_deletion	Exon 3 of 13	NP_001364334.1	O15265-1
	ATXN7	NM_001177387.1		c.107_118delAGCAGCAGCAGC	p.Gln36_Gln39del	disruptive_inframe_deletion	Exon 2 of 13	NP_001170858.1	O15265-2
	ATXN7	NM_000333.4		c.107_118delAGCAGCAGCAGC	p.Gln36_Gln39del	disruptive_inframe_deletion	Exon 3 of 13	NP_000324.1	O15265-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN7	ENST00000674280.1	MANE Select	c.107_118delAGCAGCAGCAGC	p.Gln36_Gln39del	disruptive_inframe_deletion	Exon 3 of 13	ENSP00000501377.1	O15265-1
	ATXN7	ENST00000295900.10	TSL:1	c.107_118delAGCAGCAGCAGC	p.Gln36_Gln39del	disruptive_inframe_deletion	Exon 3 of 13	ENSP00000295900.6	O15265-1
	ATXN7	ENST00000522345.2	TSL:2	c.107_118delAGCAGCAGCAGC	p.Gln36_Gln39del	disruptive_inframe_deletion	Exon 1 of 12	ENSP00000428067.2	O15265-2

Frequencies

GnomAD3 genomes AF: 0.000242 AC: 35 AN: 144616 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.000426

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000204

Gnomad ASJ AF: 0.000889

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000425

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000153

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000155 AC: 146 AN: 942420 Hom.: 0 AF XY: 0.000170 AC XY: 76 AN XY: 446580

African (AFR) AF: 0.000565 AC: 10 AN: 17714

American (AMR) AF: 0.00 AC: 0 AN: 5282

Ashkenazi Jewish (ASJ) AF: 0.000238 AC: 2 AN: 8396

East Asian (EAS) AF: 0.000104 AC: 1 AN: 9614

South Asian (SAS) AF: 0.000450 AC: 9 AN: 20022

European-Finnish (FIN) AF: 0.0000530 AC: 1 AN: 18856

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2094

European-Non Finnish (NFE) AF: 0.000140 AC: 116 AN: 827340

Other (OTH) AF: 0.000211 AC: 7 AN: 33102

GnomAD4 genome AF: 0.000242 AC: 35 AN: 144616 Hom.: 0 Cov.: 23 AF XY: 0.000256 AC XY: 18 AN XY: 70298

African (AFR) AF: 0.000426 AC: 17 AN: 39888

American (AMR) AF: 0.000204 AC: 3 AN: 14684

Ashkenazi Jewish (ASJ) AF: 0.000889 AC: 3 AN: 3374

East Asian (EAS) AF: 0.00 AC: 0 AN: 4780

South Asian (SAS) AF: 0.000425 AC: 2 AN: 4710

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8512

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 304

European-Non Finnish (NFE) AF: 0.000153 AC: 10 AN: 65450

Other (OTH) AF: 0.00 AC: 0 AN: 2008

Alfa AF: 0.00 Hom.: 39

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.8
Mutation Taster		=185/15	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs193922929; hg19: chr3-63898360;