chr4-184010095-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020225.3(STOX2):āc.1257T>Gā(p.Asp419Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,452,420 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020225.3 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 |
---|---|---|---|---|---|---|---|
STOX2 | NM_020225.3 | c.1257T>G | p.Asp419Glu | missense_variant | 3/4 | ENST00000308497.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STOX2 | ENST00000308497.9 | c.1257T>G | p.Asp419Glu | missense_variant | 3/4 | 1 | NM_020225.3 | P1 | |
STOX2 | ENST00000513034.3 | c.518-6994T>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1452420Hom.: 0 Cov.: 40 AF XY: 0.00 AC XY: 0AN XY: 721414
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.1257T>G (p.D419E) alteration is located in exon 3 (coding exon 3) of the STOX2 gene. This alteration results from a T to G substitution at nucleotide position 1257, causing the aspartic acid (D) at amino acid position 419 to be replaced by a glutamic acid (E). 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