8-54458195-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_022454.4(SOX17):c.57G>C(p.Ala19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,590,368 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A19A) has been classified as Likely benign.
Frequency
Consequence
NM_022454.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX17 | NM_022454.4 | c.57G>C | p.Ala19= | synonymous_variant | 1/2 | ENST00000297316.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX17 | ENST00000297316.5 | c.57G>C | p.Ala19= | synonymous_variant | 1/2 | 1 | NM_022454.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000603 AC: 12AN: 198878Hom.: 0 AF XY: 0.0000546 AC XY: 6AN XY: 109916
GnomAD4 exome AF: 0.000147 AC: 212AN: 1438020Hom.: 4 Cov.: 32 AF XY: 0.000153 AC XY: 109AN XY: 713700
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152348Hom.: 0 Cov.: 34 AF XY: 0.0000805 AC XY: 6AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at