chr1-109490969-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001350175.2(ATXN7L2):c.1502C>T(p.Pro501Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000941 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. P501R) 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>T | p.Pro501Leu | missense_variant | 10/11 | ENST00000683729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN7L2 | ENST00000683729.1 | c.1502C>T | p.Pro501Leu | missense_variant | 10/11 | NM_001350175.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000840 AC: 2AN: 238104Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 129154
GnomAD4 exome AF: 0.00000486 AC: 7AN: 1441614Hom.: 0 Cov.: 31 AF XY: 0.00000699 AC XY: 5AN XY: 715196
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.1406C>T (p.P469L) alteration is located in exon 10 (coding exon 10) of the ATXN7L2 gene. This alteration results from a C to T substitution at nucleotide position 1406, causing the proline (P) at amino acid position 469 to be replaced by a leucine (L). 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