1-204121886-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005686.3(SOX13):c.776-14T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 1,597,756 control chromosomes in the GnomAD database, including 3,268 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_005686.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX13 | NM_005686.3 | c.776-14T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000367204.6 | |||
SOX13 | XM_005245623.4 | c.773-14T>C | splice_polypyrimidine_tract_variant, intron_variant | ||||
SOX13 | XM_047435006.1 | c.776-14T>C | splice_polypyrimidine_tract_variant, intron_variant | ||||
SOX13 | XM_047435007.1 | c.773-14T>C | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX13 | ENST00000367204.6 | c.776-14T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005686.3 | P1 | |||
SOX13 | ENST00000618875.4 | c.776-14T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
SOX13 | ENST00000480326.1 | c.374T>C | p.Leu125Pro | missense_variant, NMD_transcript_variant | 4/6 | 5 | |||
SOX13 | ENST00000272193.10 | n.643-14T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0891 AC: 13557AN: 152072Hom.: 1054 Cov.: 32
GnomAD3 exomes AF: 0.0464 AC: 11457AN: 246716Hom.: 494 AF XY: 0.0442 AC XY: 5921AN XY: 134054
GnomAD4 exome AF: 0.0466 AC: 67317AN: 1445566Hom.: 2213 Cov.: 30 AF XY: 0.0456 AC XY: 32845AN XY: 720064
GnomAD4 genome AF: 0.0893 AC: 13583AN: 152190Hom.: 1055 Cov.: 32 AF XY: 0.0857 AC XY: 6381AN XY: 74418
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at