rs752911521
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PVS1_StrongBS2
The ENST00000252934.10(ATXN10):c.647+1_647+2insT variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.00000682 in 1,613,518 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000252934.10 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN10 | NM_013236.4 | c.647+2dupT | splice_region_variant, intron_variant | Intron 5 of 11 | ENST00000252934.10 | NP_037368.1 | ||
ATXN10 | NM_001167621.2 | c.455+2dupT | splice_region_variant, intron_variant | Intron 4 of 10 | NP_001161093.1 | |||
ATXN10 | XM_047441314.1 | c.647+2dupT | splice_region_variant, intron_variant | Intron 5 of 11 | XP_047297270.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN10 | ENST00000252934.10 | c.647+1_647+2insT | splice_donor_variant, intron_variant | Intron 5 of 11 | 1 | NM_013236.4 | ENSP00000252934.4 | |||
ATXN10 | ENST00000381061.8 | c.455+1_455+2insT | splice_donor_variant, intron_variant | Intron 4 of 10 | 2 | ENSP00000370449.4 | ||||
ATXN10 | ENST00000498009.5 | n.821+1_821+2insT | splice_donor_variant, intron_variant | Intron 5 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251356Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135872
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461292Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726972
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74374
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.647+2dupT intronic alteration consists of a duplication of T two nucleotides after exon 5 of the ATXN10 gene. Alterations that disrupt the canonical splice donor site are typically deleterious in nature (Richards, 2015). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at