6-16327684-ATGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-ATGCTGCTGCTGCTGCTGC

Position:

• chr6-16327684-ATGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-ATGCTGCTGCTGCTGCTGC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001128164.2(ATXN1):​c.615_626del​(p.Gln205_Gln208del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000202 in 1,474,032 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00061 (1 hom., cov: 20)
  • Exomes 𝑓: 0.00016 (0 hom.)
• Consequence: ATXN1 NM_001128164.2 inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

ATXN1 (HGNC:10548): (ataxin 1) 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. The function of the ataxins is not known. This locus has been mapped to chromosome 6, and it has been determined that the diseased allele contains 40-83 CAG repeats, compared to 6-39 in the normal allele, and is associated with spinocerebellar ataxia type 1 (SCA1). Alternative splicing results in multiple transcript variants, with one variant encoding multiple distinct proteins, ATXN1 and Alt-ATXN1, due to the use of overlapping alternate reading frames. [provided by RefSeq, Nov 2017]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 82 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN1	NM_001128164.2	c.615_626del	p.Gln205_Gln208del	inframe_deletion	7/8	ENST00000436367.6	NP_001121636.1
ATXN1	NM_000332.4	c.615_626del	p.Gln205_Gln208del	inframe_deletion	8/9		NP_000323.2
ATXN1	NM_001357857.2	c.*28_*39del		3_prime_UTR_variant	8/9		NP_001344786.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN1	ENST00000436367.6	c.615_626del	p.Gln205_Gln208del	inframe_deletion	7/8	1	NM_001128164.2	ENSP00000416360	P1
ATXN1	ENST00000244769.8	c.615_626del	p.Gln205_Gln208del	inframe_deletion	8/9	1		ENSP00000244769	P1
ATXN1	ENST00000642969.1			downstream_gene_variant				ENSP00000493530

Frequencies

GnomAD3 genomes AF: 0.000609 AC: 82 AN: 134636 Hom.: 1 Cov.: 20

Gnomad AFR AF: 0.00144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000902

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00272

Gnomad SAS AF: 0.000758

Gnomad FIN AF: 0.000204

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000929

Gnomad OTH AF: 0.000551

GnomAD4 exome AF: 0.000161 AC: 216 AN: 1339298 Hom.: 0 AF XY: 0.000173 AC XY: 115 AN XY: 665408

Gnomad4 AFR exome AF: 0.000603

Gnomad4 AMR exome AF: 0.000423

Gnomad4 ASJ exome AF: 0.0000402

Gnomad4 EAS exome AF: 0.00226

Gnomad4 SAS exome AF: 0.000242

Gnomad4 FIN exome AF: 0.0000249

Gnomad4 NFE exome AF: 0.0000802

Gnomad4 OTH exome AF: 0.000218

GnomAD4 genome AF: 0.000609 AC: 82 AN: 134734 Hom.: 1 Cov.: 20 AF XY: 0.000565 AC XY: 37 AN XY: 65504

Gnomad4 AFR AF: 0.00143

Gnomad4 AMR AF: 0.000901

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00273

Gnomad4 SAS AF: 0.000758

Gnomad4 FIN AF: 0.000204

Gnomad4 NFE AF: 0.0000929

Gnomad4 OTH AF: 0.000545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs193922926; hg19: chr6-16327915;