chr3-63912815-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001377405.1(ATXN7):c.217G>A(p.Ala73Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000424 in 1,414,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001377405.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN7 | NM_001377405.1 | c.217G>A | p.Ala73Thr | missense_variant | 3/13 | ENST00000674280.1 | |
ATXN7 | NM_001177387.1 | c.217G>A | p.Ala73Thr | missense_variant | 2/13 | ||
ATXN7 | NM_000333.4 | c.217G>A | p.Ala73Thr | missense_variant | 3/13 | ||
ATXN7 | NM_001377406.1 | c.217G>A | p.Ala73Thr | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN7 | ENST00000674280.1 | c.217G>A | p.Ala73Thr | missense_variant | 3/13 | NM_001377405.1 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000424 AC: 6AN: 1414172Hom.: 0 Cov.: 33 AF XY: 0.00000142 AC XY: 1AN XY: 703558
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.217G>A (p.A73T) alteration is located in exon 2 (coding exon 1) of the ATXN7 gene. This alteration results from a G to A substitution at nucleotide position 217, causing the alanine (A) at amino acid position 73 to be replaced by a threonine (T). 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