chrX-140503972-GGCTGCGGCCGCA-G
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP3BP6_ModerateBS2
The NM_005634.3(SOX3):βc.1077_1088delβ(p.Ala361_Ala364del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,048,582 control chromosomes in the GnomAD database, including 1 homozygotes. There are 30 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (β ).
Frequency
Genomes: π 0.000064 ( 0 hom., 2 hem., cov: 23)
Exomes π: 0.00013 ( 1 hom. 28 hem. )
Consequence
SOX3
NM_005634.3 inframe_deletion
NM_005634.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.44
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 -7 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_005634.3
BP6
Variant X-140503972-GGCTGCGGCCGCA-G is Benign according to our data. Variant chrX-140503972-GGCTGCGGCCGCA-G is described in ClinVar as [Likely_benign]. Clinvar id is 2661539.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAd4 at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX3 | NM_005634.3 | c.1077_1088del | p.Ala361_Ala364del | inframe_deletion | 1/1 | ENST00000370536.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX3 | ENST00000370536.5 | c.1077_1088del | p.Ala361_Ala364del | inframe_deletion | 1/1 | NM_005634.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000640 AC: 7AN: 109296Hom.: 0 Cov.: 23 AF XY: 0.0000618 AC XY: 2AN XY: 32374
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GnomAD3 exomes AF: 0.0000803 AC: 4AN: 49817Hom.: 0 AF XY: 0.0000821 AC XY: 1AN XY: 12185
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GnomAD4 exome AF: 0.000128 AC: 120AN: 939286Hom.: 1 AF XY: 0.0000972 AC XY: 28AN XY: 288012
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GnomAD4 genome AF: 0.0000640 AC: 7AN: 109296Hom.: 0 Cov.: 23 AF XY: 0.0000618 AC XY: 2AN XY: 32374
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | SOX3: BS2 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at