chr11-16018629-A-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_001367873.1(SOX6):c.1624-3579T>A variant causes a intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0742 in 152,108 control chromosomes in the GnomAD database, including 858 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.074 ( 858 hom., cov: 32)
Consequence
SOX6
NM_001367873.1 intron
NM_001367873.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 8.55
Genes affected
SOX6 (HGNC:16421): (SRY-box transcription factor 6) This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. The encoded protein is a transcriptional activator that is required for normal development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells. The encoded protein interacts with other family members to cooperatively activate gene expression. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BP6
Variant 11-16018629-A-T is Benign according to our data. Variant chr11-16018629-A-T is described in ClinVar as [Benign]. Clinvar id is 1286591.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX6 | NM_001367873.1 | c.1624-3579T>A | intron_variant | ENST00000683767.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX6 | ENST00000683767.1 | c.1624-3579T>A | intron_variant | NM_001367873.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0742 AC: 11282AN: 151988Hom.: 857 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0742 AC: 11290AN: 152108Hom.: 858 Cov.: 32 AF XY: 0.0787 AC XY: 5852AN XY: 74348
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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 02, 2020 | This variant is associated with the following publications: (PMID: 29518216) - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at