Genetic Variant ATXN10:c.1174-11589_1174-11535dupATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT (chr22-45795354-G-GATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_013236.4(ATXN10):c.1174-11589_1174-11535dupATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_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: not found (cov: 0)

Consequence

ATXN10
NM_013236.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.237

Publications

1 publications found

Variant links:

Genes affected

ATXN10 (HGNC:10549): (ataxin 10) This gene encodes a protein that may function in neuron survival, neuron differentiation, and neuritogenesis. These roles may be carried out via activation of the mitogen-activated protein kinase cascade. Expansion of an ATTCT repeat from 9-32 copies to 800-4500 copies in an intronic region of this locus has been associated with spinocerebellar ataxia, type 10. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jul 2016]

ATXN10 Gene-Disease associations (from GenCC):

spinocerebellar ataxia type 10
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ATXN10 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013236.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN10	NM_013236.4	MANE Select	c.1174-11589_1174-11535dupATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT		intron	N/A	NP_037368.1
	ATXN10	NM_001167621.2		c.982-11589_982-11535dupATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT		intron	N/A	NP_001161093.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ATXN10	ENST00000252934.10	TSL:1 MANE Select	c.1174-11605_1174-11604insATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT	intron	N/A	ENSP00000252934.4
ATXN10	ENST00000381061.8	TSL:2	c.982-11605_982-11604insATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT	intron	N/A	ENSP00000370449.4
ATXN10	ENST00000435026.5	TSL:3	c.430-11605_430-11604insATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT	intron	N/A	ENSP00000391117.1

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.24

Splicing

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

Publications

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22-45795354-GATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT-GATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over