X-140504005-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_005634.3(SOX3):c.1056C>A(p.Pro352=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 988,065 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., 4 hem., cov: 23)
Exomes 𝑓: 0.000014 ( 0 hom. 5 hem. )
Consequence
SOX3
NM_005634.3 synonymous
NM_005634.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.00
Genes affected
SOX3 (HGNC:11199): (SRY-box transcription factor 3) 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. Mutations in this gene have been associated with X-linked cognitive disability with growth hormone deficiency. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant X-140504005-G-T is Benign according to our data. Variant chrX-140504005-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3041100.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=1 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX3 | NM_005634.3 | c.1056C>A | p.Pro352= | synonymous_variant | 1/1 | ENST00000370536.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX3 | ENST00000370536.5 | c.1056C>A | p.Pro352= | synonymous_variant | 1/1 | NM_005634.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000128 AC: 14AN: 109647Hom.: 0 Cov.: 23 AF XY: 0.000123 AC XY: 4AN XY: 32587
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GnomAD4 exome AF: 0.0000137 AC: 12AN: 878389Hom.: 0 Cov.: 22 AF XY: 0.0000187 AC XY: 5AN XY: 266903
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GnomAD4 genome AF: 0.000128 AC: 14AN: 109676Hom.: 0 Cov.: 23 AF XY: 0.000123 AC XY: 4AN XY: 32630
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SOX3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at