chr3-63912702-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001377405.1(ATXN7):c.104A>C(p.Gln35Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00222 in 1,185,296 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001377405.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN7 | NM_001377405.1 | c.104A>C | p.Gln35Pro | missense_variant | 3/13 | ENST00000674280.1 | |
ATXN7 | NM_001177387.1 | c.104A>C | p.Gln35Pro | missense_variant | 2/13 | ||
ATXN7 | NM_000333.4 | c.104A>C | p.Gln35Pro | missense_variant | 3/13 | ||
ATXN7 | NM_001377406.1 | c.104A>C | p.Gln35Pro | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN7 | ENST00000674280.1 | c.104A>C | p.Gln35Pro | missense_variant | 3/13 | NM_001377405.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00140 AC: 207AN: 147518Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.000504 AC: 14AN: 27758Hom.: 0 AF XY: 0.000388 AC XY: 6AN XY: 15476
GnomAD4 exome AF: 0.00234 AC: 2427AN: 1037676Hom.: 3 Cov.: 32 AF XY: 0.00224 AC XY: 1113AN XY: 496300
GnomAD4 genome ? AF: 0.00140 AC: 207AN: 147620Hom.: 2 Cov.: 31 AF XY: 0.00117 AC XY: 84AN XY: 71860
ClinVar
Submissions by phenotype
ATXN7-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at