22-45672074-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_013236.4(ATXN10):āc.11C>Gā(p.Pro4Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000065 in 1,537,420 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_013236.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN10 | NM_013236.4 | c.11C>G | p.Pro4Arg | missense_variant | 1/12 | ENST00000252934.10 | |
ATXN10 | NM_001167621.2 | c.11C>G | p.Pro4Arg | missense_variant | 1/11 | ||
ATXN10 | XM_047441314.1 | c.11C>G | p.Pro4Arg | missense_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN10 | ENST00000252934.10 | c.11C>G | p.Pro4Arg | missense_variant | 1/12 | 1 | NM_013236.4 | P1 | |
ENST00000623075.1 | n.15056C>G | non_coding_transcript_exon_variant | 1/1 | ||||||
ATXN10 | ENST00000381061.8 | c.11C>G | p.Pro4Arg | missense_variant | 1/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000731 AC: 1AN: 136832Hom.: 0 AF XY: 0.0000134 AC XY: 1AN XY: 74520
GnomAD4 exome AF: 0.00000217 AC: 3AN: 1385302Hom.: 0 Cov.: 31 AF XY: 0.00000439 AC XY: 3AN XY: 683682
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74308
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.11C>G (p.P4R) alteration is located in exon 1 (coding exon 1) of the ATXN10 gene. This alteration results from a C to G substitution at nucleotide position 11, causing the proline (P) at amino acid position 4 to be replaced by an arginine (R). 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