chr1-109488988-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001350175.2(ATXN7L2):c.1021C>T(p.Arg341Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,614,046 control chromosomes in the GnomAD database, including 1 homozygotes. 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_001350175.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN7L2 | NM_001350175.2 | c.1021C>T | p.Arg341Cys | missense_variant | 7/11 | ENST00000683729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN7L2 | ENST00000683729.1 | c.1021C>T | p.Arg341Cys | missense_variant | 7/11 | NM_001350175.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250542Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135504
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461830Hom.: 1 Cov.: 31 AF XY: 0.0000564 AC XY: 41AN XY: 727214
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.925C>T (p.R309C) alteration is located in exon 7 (coding exon 7) of the ATXN7L2 gene. This alteration results from a C to T substitution at nucleotide position 925, causing the arginine (R) at amino acid position 309 to be replaced by a cysteine (C). 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