22-45795354-GATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT-GATTCTATTCTATTCTATTCTATTCTATTCTATTCT

Position:

• chr22-45795354-GATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT-GATTCTATTCTATTCTATTCTATTCTATTCTATTCT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_013236.4(ATXN10):​c.1174-11544_1174-11535delATTCTATTCT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1111 hom., cov: 0)
• Consequence: ATXN10 NM_013236.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN10	NM_013236.4	c.1174-11544_1174-11535delATTCTATTCT		intron_variant		ENST00000252934.10	NP_037368.1
ATXN10	NM_001167621.2	c.982-11544_982-11535delATTCTATTCT		intron_variant			NP_001161093.1
ATXN10	XM_047441314.1	c.1174-11544_1174-11535delATTCTATTCT		intron_variant			XP_047297270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN10	ENST00000252934.10	c.1174-11604_1174-11595delATTCTATTCT		intron_variant		1	NM_013236.4	ENSP00000252934.4

Frequencies

GnomAD3 genomes AF: 0.136 AC: 17146 AN: 126448 Hom.: 1111 Cov.: 0

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0771

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.136 AC: 17150 AN: 126554 Hom.: 1111 Cov.: 0 AF XY: 0.137 AC XY: 8358 AN XY: 60796

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0765

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.161

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: rs60726084; hg19: chr22-46191234;