chr1-109490969-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001350175.2(ATXN7L2):c.1502C>G(p.Pro501Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 1,593,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P501L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001350175.2 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 |
---|---|---|---|---|---|---|---|
ATXN7L2 | NM_001350175.2 | c.1502C>G | p.Pro501Arg | missense_variant | 10/11 | ENST00000683729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN7L2 | ENST00000683729.1 | c.1502C>G | p.Pro501Arg | missense_variant | 10/11 | NM_001350175.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000210 AC: 5AN: 238104Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 129154
GnomAD4 exome AF: 0.0000194 AC: 28AN: 1441614Hom.: 0 Cov.: 31 AF XY: 0.0000126 AC XY: 9AN XY: 715196
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.1406C>G (p.P469R) alteration is located in exon 10 (coding exon 10) of the ATXN7L2 gene. This alteration results from a C to G substitution at nucleotide position 1406, causing the proline (P) at amino acid position 469 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