chrX-140503968-T-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_005634.3(SOX3):āc.1093A>Cā(p.Met365Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000807 in 1,053,436 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_005634.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX3 | NM_005634.3 | c.1093A>C | p.Met365Leu | missense_variant | 1/1 | ENST00000370536.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX3 | ENST00000370536.5 | c.1093A>C | p.Met365Leu | missense_variant | 1/1 | NM_005634.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000465 AC: 50AN: 107538Hom.: 0 Cov.: 23 AF XY: 0.000541 AC XY: 17AN XY: 31414
GnomAD3 exomes AF: 0.0000329 AC: 2AN: 60760Hom.: 0 AF XY: 0.0000661 AC XY: 1AN XY: 15140
GnomAD4 exome AF: 0.0000370 AC: 35AN: 945864Hom.: 0 Cov.: 30 AF XY: 0.00000346 AC XY: 1AN XY: 288878
GnomAD4 genome AF: 0.000465 AC: 50AN: 107572Hom.: 0 Cov.: 23 AF XY: 0.000540 AC XY: 17AN XY: 31456
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at