13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Position:

• chr13-70139383-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG

Variant summary

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

The ENST00000414504.6(ATXN8OS):​n.1146_1148delTGC variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 454,152 control chromosomes in the GnomAD database, including 199 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.025 (33 hom., cov: 0)
  • Exomes 𝑓: 0.024 (166 hom.)
• Consequence: ATXN8OS ENST00000414504.6 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

ATXN8OS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN8OS	NR_002717.3	n.938_940delTGC		non_coding_transcript_exon_variant	5/5
ATXN8OS	NR_185834.1	n.454-7928_454-7926delTGC		intron_variant
ATXN8OS	NR_185835.1	n.454-7928_454-7926delTGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN8OS	ENST00000414504.6	n.1146_1148delTGC		splice_region_variant, non_coding_transcript_exon_variant	5/5	5
ENSG00000288330	ENST00000673087.1	n.46_48delCAG		non_coding_transcript_exon_variant	1/1
ATXN8OS	ENST00000660386.1	n.451-7928_451-7926delTGC		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0250 AC: 2729 AN: 108972 Hom.: 33 Cov.: 0

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.0195

Gnomad AMR AF: 0.0271

Gnomad ASJ AF: 0.0102

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.0595

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.0508

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0278

GnomAD4 exome AF: 0.0235 AC: 8119 AN: 345150 Hom.: 166 AF XY: 0.0243 AC XY: 4461 AN XY: 183850

Gnomad4 AFR exome AF: 0.0303

Gnomad4 AMR exome AF: 0.0143

Gnomad4 ASJ exome AF: 0.00843

Gnomad4 EAS exome AF: 0.0296

Gnomad4 SAS exome AF: 0.0420

Gnomad4 FIN exome AF: 0.0147

Gnomad4 NFE exome AF: 0.0227

Gnomad4 OTH exome AF: 0.0234

GnomAD4 genome AF: 0.0251 AC: 2731 AN: 109002 Hom.: 33 Cov.: 0 AF XY: 0.0250 AC XY: 1313 AN XY: 52588

Gnomad4 AFR AF: 0.0260

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0102

Gnomad4 EAS AF: 0.0209

Gnomad4 SAS AF: 0.0599

Gnomad4 FIN AF: 0.0118

Gnomad4 NFE AF: 0.0244

Gnomad4 OTH AF: 0.0290

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: rs193922930; hg19: chr13-70713515;