chr11-15972849-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4BS1_Supporting
The NM_001367873.1(SOX6):c.2447G>A(p.Ser816Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S816S) has been classified as Likely benign.
Frequency
Consequence
NM_001367873.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX6 | NM_001367873.1 | c.2447G>A | p.Ser816Asn | missense_variant | 16/16 | ENST00000683767.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX6 | ENST00000683767.1 | c.2447G>A | p.Ser816Asn | missense_variant | 16/16 | NM_001367873.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250574Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135358
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727232
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2022 | The c.2387G>A (p.S796N) alteration is located in exon 16 (coding exon 15) of the SOX6 gene. This alteration results from a G to A substitution at nucleotide position 2387, causing the serine (S) at amino acid position 796 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