chr4-184010535-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_020225.3(STOX2):c.1697C>T(p.Pro566Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,613,876 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020225.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STOX2 | ENST00000308497.9 | c.1697C>T | p.Pro566Leu | missense_variant | Exon 3 of 4 | 1 | NM_020225.3 | ENSP00000311257.4 | ||
STOX2 | ENST00000513034.3 | c.518-6554C>T | intron_variant | Intron 2 of 2 | 3 | ENSP00000422118.3 | ||||
STOX2 | ENST00000506529.1 | c.-239C>T | upstream_gene_variant | 1 | ENSP00000426209.1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152232Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000185 AC: 46AN: 248414 AF XY: 0.000215 show subpopulations
GnomAD4 exome AF: 0.000124 AC: 181AN: 1461526Hom.: 1 Cov.: 39 AF XY: 0.000136 AC XY: 99AN XY: 727032 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000230 AC: 35AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74506 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1697C>T (p.P566L) alteration is located in exon 3 (coding exon 3) of the STOX2 gene. This alteration results from a C to T substitution at nucleotide position 1697, causing the proline (P) at amino acid position 566 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