DUP chr7:72,846,244-74,187,855
CNV summary
Our verdict is Uncertain significance. Variant got ACMG score 0.
CNV gain of the region 7:72,846,244-74,187,855 (1.3 mb), is localized in (7)(q11.23). The region contains protein-coding and important regions. There is complete overlap with established TS region(s): dbVar:nssv15119921. However, all these regions lay inside a transcript, the mechanism of pathogenicity is that they probably break it. There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50 (and 16 more) in the affected region.
Genes
TODOClinGen
TODOACMG Results
Pathogenicity Level: Uncertain_significance
Score: 0
Criteria:
- GAIN_1A : 0 pointsRule : Contains protein-coding or other known functionally important elements.Details:The region contains protein-coding genes, for example: EIF4H. The region contains important regions, for example: dbVar:nssv15137072.
- GAIN_2A Beware, not metRule (not met) : Complete overlap; the known pathogenic gain SV is fully contained within the observed copy-number gain.Details:There is complete overlap with established TS region(s): dbVar:nssv15119921. However, all these regions lay inside a transcript, the mechanism of pathogenicity is that they probably break it.
- GAIN_2D Beware, not metRule (not met) : Smaller than established benign copy-number gain, breakpoint(s) does not interrupt protein-coding genes.Details:Breakpoint probably interrupts genes EIF4H, LIMK1, ELN, TMEM270, METTL27, CLDN4, CLDN3, ABHD11, STX1A, BUD23, DNAJC30, VPS37D, MLXIPL, TBL2, BCL7B, BAZ1B, FZD9, FKBP6, TRIM50, NSUN5, SPDYE10, SPDYE9, SPDYE11, SPDYE8, TRIM74, POM121
- GAIN_2E : 0 pointsRule : Smaller than established benign copy-number gain, breakpoint(s) potentially interrupts protein-coding gene.Details:Contained in established TS region 1000g, DDD:24479, dbVar, DDD:24478, dbVar, dbVar, probably breaking EIF4H, LIMK1, ELN, TMEM270, METTL27, CLDN4, CLDN3, ABHD11, STX1A, BUD23, DNAJC30, VPS37D, MLXIPL, TBL2, BCL7B, BAZ1B, FZD9, FKBP6, TRIM50, NSUN5, SPDYE10, SPDYE9, SPDYE11, SPDYE8, TRIM74, POM121
- GAIN_3A : 0 pointsRule : 0–34 genesDetails:There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50, FKBP6, FZD9, BAZ1B, BCL7B, TBL2, MLXIPL, VPS37D, DNAJC30, BUD23, STX1A, ABHD11, CLDN3, CLDN4, METTL27, TMEM270, EIF4H
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{
"cnvChange": {
"chr": "7",
"start": 72846244,
"end": 74187855,
"svType": "DUP"
},
"annotations": {
"chr": "7",
"start": 72846244,
"end": 74187855,
"svType": "DUP",
"length": 1341611,
"geneGroups": [
"Nucleoporins",
"Tripartite motif family|Ring finger proteins",
"Speedy/RINGO cell cycle regulator family",
"NOP2/Sun RNA methyltransferase family",
"FKBP prolyl isomerases",
"CD molecules|G protein-coupled receptors, Class F frizzled",
"PHD finger proteins|Bromodomain containing|B-WICH chromatin-remodelling complex subunits",
"BAF complex",
"WD repeat domain containing",
"Basic helix-loop-helix proteins",
"ESCRT-I",
"DNAJ (HSP40) heat shock proteins",
"Ribosomal biogenesis factors|7BS DNA/RNA methyltransferases",
"Syntaxins",
"Abhydrolase domain containing",
"Claudins",
"7BS orphan methyltransferases",
"LIM domain containing|PDZ domain containing|LIMK/TESK kinase family",
"RNA binding motif containing|MicroRNA protein coding host genes"
],
"cytobandString": "(7)(q11.23)",
"overlappedGenes": [
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},
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"readingFrameDestroyed": true,
"overlapType": "FIVE_UTR_WITH_CDS",
"numberOfPLpVariantsCovered": 0,
"escapeNmd": false
}
},
{
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"clingenHi": "NO_EVIDENCE_AVAILABLE",
"clingenTs": "NO_EVIDENCE_AVAILABLE",
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},
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},
"triploinsufficiencyType": "NO_EVIDENCE_AVAILABLE",
"haploinsufficiencyType": "NO_EVIDENCE_AVAILABLE"
},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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},
{
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{
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},
{
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},
{
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},
{
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},
{
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},
"acmg": {
"position": {
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"end": 74187855
},
"criteria": [
{
"criterium": "GAIN_1A",
"points": 0
},
{
"criterium": "GAIN_2E",
"points": 0
},
{
"criterium": "GAIN_3A",
"points": 0
}
],
"criteriaReports": [
{
"criterium": "GAIN_1A",
"report": "The region contains protein-coding genes, for example: EIF4H. The region contains important regions, for example: dbVar:nssv15137072. "
},
{
"criterium": "GAIN_2A",
"report": "There is complete overlap with established TS region(s): dbVar:nssv15119921. However, all these regions lay inside a transcript, the mechanism of pathogenicity is that they probably break it. "
},
{
"criterium": "GAIN_2D",
"report": "Breakpoint probably interrupts genes EIF4H, LIMK1, ELN, TMEM270, METTL27, CLDN4, CLDN3, ABHD11, STX1A, BUD23, DNAJC30, VPS37D, MLXIPL, TBL2, BCL7B, BAZ1B, FZD9, FKBP6, TRIM50, NSUN5, SPDYE10, SPDYE9, SPDYE11, SPDYE8, TRIM74, POM121"
},
{
"criterium": "GAIN_2E",
"report": "Contained in established TS region 1000g, DDD:24479, dbVar, DDD:24478, dbVar, dbVar, probably breaking EIF4H, LIMK1, ELN, TMEM270, METTL27, CLDN4, CLDN3, ABHD11, STX1A, BUD23, DNAJC30, VPS37D, MLXIPL, TBL2, BCL7B, BAZ1B, FZD9, FKBP6, TRIM50, NSUN5, SPDYE10, SPDYE9, SPDYE11, SPDYE8, TRIM74, POM121"
},
{
"criterium": "GAIN_3A",
"report": "There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50, FKBP6, FZD9, BAZ1B, BCL7B, TBL2, MLXIPL, VPS37D, DNAJC30, BUD23, STX1A, ABHD11, CLDN3, CLDN4, METTL27, TMEM270, EIF4H"
}
],
"criteriaData": [
{
"criterium": "GAIN_1A",
"report": "The region contains protein-coding genes, for example: EIF4H. The region contains important regions, for example: dbVar:nssv15137072. ",
"met": true,
"points": 0
},
{
"criterium": "GAIN_2A",
"report": "There is complete overlap with established TS region(s): dbVar:nssv15119921. However, all these regions lay inside a transcript, the mechanism of pathogenicity is that they probably break it. ",
"met": false,
"points": null
},
{
"criterium": "GAIN_2D",
"report": "Breakpoint probably interrupts genes EIF4H, LIMK1, ELN, TMEM270, METTL27, CLDN4, CLDN3, ABHD11, STX1A, BUD23, DNAJC30, VPS37D, MLXIPL, TBL2, BCL7B, BAZ1B, FZD9, FKBP6, TRIM50, NSUN5, SPDYE10, SPDYE9, SPDYE11, SPDYE8, TRIM74, POM121",
"met": false,
"points": null
},
{
"criterium": "GAIN_2E",
"report": "Contained in established TS region 1000g, DDD:24479, dbVar, DDD:24478, dbVar, dbVar, probably breaking EIF4H, LIMK1, ELN, TMEM270, METTL27, CLDN4, CLDN3, ABHD11, STX1A, BUD23, DNAJC30, VPS37D, MLXIPL, TBL2, BCL7B, BAZ1B, FZD9, FKBP6, TRIM50, NSUN5, SPDYE10, SPDYE9, SPDYE11, SPDYE8, TRIM74, POM121",
"met": true,
"points": 0
},
{
"criterium": "GAIN_3A",
"report": "There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50, FKBP6, FZD9, BAZ1B, BCL7B, TBL2, MLXIPL, VPS37D, DNAJC30, BUD23, STX1A, ABHD11, CLDN3, CLDN4, METTL27, TMEM270, EIF4H",
"met": true,
"points": 0
}
],
"report": "CNV gain of the region 7:72,846,244-74,187,855 (1.3 mb), is localized in (7)(q11.23). The region contains protein-coding and important regions. There is complete overlap with established TS region(s): dbVar:nssv15119921. However, all these regions lay inside a transcript, the mechanism of pathogenicity is that they probably break it. There are 26 protein coding genes across 21 gene families: ELN, LIMK1, POM121, TRIM74, SPDYE8, SPDYE11, SPDYE9, SPDYE10, NSUN5, TRIM50 (and 16 more) in the affected region. ",
"pathogenicityLevel": "Uncertain_significance",
"score": 0,
"svType": "DUP",
"phenotype": null
}
}