X-140504059-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005634.3(SOX3):c.1002G>A(p.Gly334Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000824 in 983,027 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 30 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.000090 ( 0 hom. 30 hem. )
Consequence
SOX3
NM_005634.3 synonymous
NM_005634.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.433
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant X-140504059-C-T is Benign according to our data. Variant chrX-140504059-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3710199.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-140504059-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.433 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 30 XL gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000184 AC: 2AN: 108816Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32198
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GnomAD3 exomes AF: 0.0000751 AC: 1AN: 13321Hom.: 0 AF XY: 0.000596 AC XY: 1AN XY: 1677
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GnomAD4 exome AF: 0.0000904 AC: 79AN: 874211Hom.: 0 Cov.: 28 AF XY: 0.000112 AC XY: 30AN XY: 268713
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GnomAD4 genome AF: 0.0000184 AC: 2AN: 108816Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32198
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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
Aug 05, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at