chr8-54458520-C-CAG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_022454.4(SOX17):c.307+75_307+76insAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,558,862 control chromosomes in the GnomAD database, including 35,924 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 3367 hom., cov: 30)
Exomes 𝑓: 0.20 ( 32557 hom. )
Consequence
SOX17
NM_022454.4 intron
NM_022454.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.690
Genes affected
SOX17 (HGNC:18122): (SRY-box transcription factor 17) This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 8-54458520-C-CAG is Benign according to our data. Variant chr8-54458520-C-CAG is described in ClinVar as [Benign]. Clinvar id is 1259489.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX17 | NM_022454.4 | c.307+75_307+76insAG | intron_variant | ENST00000297316.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX17 | ENST00000297316.5 | c.307+75_307+76insAG | intron_variant | 1 | NM_022454.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.197 AC: 29916AN: 152106Hom.: 3368 Cov.: 30
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GnomAD4 exome AF: 0.204 AC: 286543AN: 1406638Hom.: 32557 AF XY: 0.207 AC XY: 144738AN XY: 698858
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GnomAD4 genome ? AF: 0.197 AC: 29929AN: 152224Hom.: 3367 Cov.: 30 AF XY: 0.204 AC XY: 15142AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at