22-45795354-GATTCT-G

Position:

• chr22-45795354-GATTCT-G

Variant summary

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

The ENST00000252934.10(ATXN10):​c.1174-11539_1174-11535del 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 0.25 (3981 hom., cov: 0)
• Consequence: ATXN10 ENST00000252934.10 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 = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN10	NM_013236.4	c.1174-11539_1174-11535del		intron_variant		ENST00000252934.10	NP_037368.1
ATXN10	NM_001167621.2	c.982-11539_982-11535del		intron_variant			NP_001161093.1
ATXN10	XM_047441314.1	c.1174-11539_1174-11535del		intron_variant			XP_047297270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN10	ENST00000252934.10	c.1174-11539_1174-11535del		intron_variant		1	NM_013236.4	ENSP00000252934	P1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 32187 AN: 126302 Hom.: 3977 Cov.: 0

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.255 AC: 32219 AN: 126408 Hom.: 3981 Cov.: 0 AF XY: 0.248 AC XY: 15067 AN XY: 60706

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.233

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;