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Please note that these adapted criteria are not currently designed to classify variants relative to non-RASopathy phenotypes (e.g. loss of function variants in PTPN11 related to metachondromatosis); however, information about these other genotype:phenotype correlations are noted within the supplemental material. These criteria are also not designed to classify somatic variation in these genes. It is well-known that information about known somatic mutations can be utilized as supporting evidence for classifying variants relative to the RASopathy spectrum disorders given the disease mechanisms are directly correlated. Future initiatives in conjunction with the ClinGen somatic working group will aim to define this relationship in subsequent versions of this documentation. 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modified so it is clear the supplementary document applies to the SVI recommendation and not the animal model section\n* PS4’s upper margins were modified to make it clear that curators should not round off any of the values in Table 2A since it is not possible to obtain a value that is .99 or .49\n* BA1 and BS1 calculations corrected, rational provided in supplement\n* BS2 modified to make it clear that either homozygous instances in gnomAD or phenotyped family members can be utilized for this criterion\n* BP2 modified to indicate that this criterion can be used for either a cis or trans variant\n* BP4 modified to be consistent with detailed description provided later in the document", "shortTitle": "Brain Malformations Specification", "specificationSource": "https://clinicalgenome.org/docs/clingen-brain-malformations-expert-panel-specifications-to-the-acmg-amp-variant-interpretation-guidelines-version-1.1/", "states": [ { "current": true, "event": { "name": "cspec-released", 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false, "event": { "name": "classified-rules-submitted", "prevState": "Classification Rules In Prep", "timeStamp": "2023-06-08T14:33:57.587Z" }, "name": "Classification Rules Submitted" }, { "current": false, "event": { "name": "classified-rules-reviewed", "prevState": "Classification Rules Submitted", "timeStamp": "2022-12-06T16:51:27.119Z" }, "name": "Classification Rules In Prep" }, { "current": false, "event": { "name": "classified-rules-withdrawn", "prevState": "Classification Rules Submitted", "timeStamp": "2023-06-08T14:30:32.836Z" }, "name": "Classification Rules In Prep" }, { "current": true, "event": { "name": "classified-rules-approved", "prevState": "Classification Rules Submitted", "timeStamp": "2023-09-06T21:13:31.945Z" }, "name": "Pilot Rules In Prep" } ], "tagNameSpaces": [ "087" ], "title": "ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MRAS Version 1.0.0", "version": "1.0.0", "versioned": true }, "entId": "GN087", "entType": "SequenceVariantInterpretation", "ld": { "Disease": [ { "entId": "MONDO:0018997", "entIri": "http://purl.obolibrary.org/obo/MONDO_0018997", "entType": "Disease", "ldhId": "135642024", "ldhIri": "https://genboree.org/cspec/Disease/id/135642024", "rev": "_iyozwl2---" } ], "Gene": [ { "entId": "MRAS", "entIri": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:7227", "entType": "Gene", "ldhId": "467839815", "ldhIri": "https://genboree.org/cspec/Gene/id/467839815", "rev": "_h6SHznu--E" } ], "RuleSet": [ { "entType": "RuleSet", "ldhId": "1528438503", "ldhIri": "https://genboree.org/cspec/RuleSet/id/1528438503", "rev": "_h6SHyTG--C" } ] }, "ldFor": { "Organization": [ { "entId": "50021", "entIri": "http://clinicalgenome.org/affiliation/50021", "entType": "Organization", "ldhId": "135637642", "ldhIri": "https://genboree.org/cspec/Organization/id/135637642", "rev": "_h6SHyD6--J" } ], "SequenceVariantInterpretation": [ { "entId": "GN001", "entType": 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"2023-11-24T13:46:56.766Z", "description": "The following criteria are for classic or attenuated familial adenomatous polyposis only and does not apply to Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS, MONDO:0017790).\nThe preferred transcript for coding, intronic and promoter 1A variants is NM_000038.6 (MANE transcript). The NM_001127510.2 transcript differs from NM_000038.6 in the number of \"non-coding\" exons in the 5' region, which results in different exon numbering (in NM_000038.6 there is only one non-coding exon, in NM_001127510.2 there is one additional non-coding exon and one non-coding exon overlapping with NM_000038.6; the 15 coding exons are the same). For the promoter 1B deletion the preferred transcript is NM_001127511.3, which has an alternative coding exon 1. The LRG_130 summarizes all three “additional” exons of the previously mentioned transcripts, resulting in 18 exons). To standardize, variants in this document are described in HGVS nomenclature according to their positions in the NM_000038.6 transcript unless otherwise specified. Numbered exons in this document refers to exons 1-16 in the NM_000038.6transcript. Refer to Supplementary Table 1 for exon number conversions. \nIt is important to note that these criteria are not developed for low/moderate penetrant variants (e. g. c.3920T>A p.(Ile1307Lys) and c.3949G>C p.(Glu1317Gln)).", "namespace": "GN089", "releaseNotes": "* Correction of some inaccuracies in the Rules for Combining Criteria.\n* Addition of some relevant instructions out of the supplementary material\n* Change in Fig. 1A: Update of the possible pathways for “G to non-G changes”\n* Change in Fig. 1B: Transfer of splice variants c.136-1G>A,C,T; c.136-2A>C,G,T; c.220+1G>A,C,T and c.220+2T>A,C,G from List E to List A and transfer of c.220G>A,C,T  from List E to List B based on RNA and phenotype data\n* Update of the supplementary material file.", "releasedUnderRevision": true, "shortTitle": "InSiGHT Hereditary Colorectal Cancer/Polyposis Specification", "specificationSource": "", "states": [ { "current": false, "event": { "modifiedBy": "xiaoyuyin", "name": "cspec-created", 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"timeStamp": "2023-09-14T10:53:29.300Z" }, "name": "Pilot Rules In Prep" }, { "current": false, "event": { "modifiedBy": "sharriso", "name": "pilot-rules-reviewed", "prevState": "Pilot Rules Submitted", "timeStamp": "2023-10-17T17:10:15.332Z" }, "name": "Pilot Rules In Prep" }, { "current": false, "event": { "modifiedBy": "ispier", "name": "pilot-rules-withdrawn", "prevState": "Pilot Rules Submitted", "timeStamp": "2023-10-20T13:04:16.330Z" }, "name": "Pilot Rules In Prep" } ], "tagNameSpaces": [ "089" ], "title": "ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for APC Version 2.1.0", "version": "2.1.0", "versioned": true }, "entId": "GN089", "entType": "SequenceVariantInterpretation", "ld": { "CriteriaCode": [ { "entType": "CriteriaCode", "ldhId": "1553527159", "ldhIri": "https://genboree.org/cspec/CriteriaCode/id/1553527159", "rev": "_h6SHxpa--I" }, { "entType": "CriteriaCode", "ldhId": 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"1553527154", "ldhIri": "https://genboree.org/cspec/CriteriaCode/id/1553527154", "rev": "_h6SHxp6--A" }, { "entType": "CriteriaCode", "ldhId": "1553527151", "ldhIri": "https://genboree.org/cspec/CriteriaCode/id/1553527151", "rev": "_h6SHxpe--1" }, { "entType": "CriteriaCode", "ldhId": "1553527146", "ldhIri": "https://genboree.org/cspec/CriteriaCode/id/1553527146", "rev": "_h6SHxpe--0" }, { "entType": "CriteriaCode", "ldhId": "1553527145", "ldhIri": "https://genboree.org/cspec/CriteriaCode/id/1553527145", "rev": "_h6SHxpe--z" }, { "entType": "CriteriaCode", "ldhId": "1553527139", "ldhIri": "https://genboree.org/cspec/CriteriaCode/id/1553527139", "rev": "_h6SHxpC--O" }, { "entType": "CriteriaCode", "ldhId": "1553527133", "ldhIri": "https://genboree.org/cspec/CriteriaCode/id/1553527133", "rev": "_h6SHxpe--w" } ], "Disease": [ { "entId": "MONDO:0021056", "entIri": "http://purl.obolibrary.org/obo/MONDO_0021056", "entType": "Disease", "ldhId": "467886956", "ldhIri": 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