chr1-204112935-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005686.3(SOX13):c.20T>A(p.Ile7Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005686.3 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 |
---|---|---|---|---|---|---|---|
SOX13 | NM_005686.3 | c.20T>A | p.Ile7Asn | missense_variant | 2/14 | ENST00000367204.6 | |
SOX13 | XM_047435006.1 | c.20T>A | p.Ile7Asn | missense_variant | 2/14 | ||
SOX13 | XM_005245623.4 | c.20T>A | p.Ile7Asn | missense_variant | 2/14 | ||
SOX13 | XM_047435007.1 | c.20T>A | p.Ile7Asn | missense_variant | 2/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX13 | ENST00000367204.6 | c.20T>A | p.Ile7Asn | missense_variant | 2/14 | 1 | NM_005686.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.20T>A (p.I7N) alteration is located in exon 2 (coding exon 1) of the SOX13 gene. This alteration results from a T to A substitution at nucleotide position 20, causing the isoleucine (I) at amino acid position 7 to be replaced by an asparagine (N). 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
Publications
No publications associated with this variant yet.