Germline Genomics Profile

This profile inlcudes 22 data elements to capture the results from germline testing. The “Cytogenetic Location” sub-profile (not shown here) groups the elements for the cytogenetic location of the germline variant detected.

Data Element	Data Type	Description	Terminology	Required
germ_report_case_id_genomic	String	The ID number from the germline report	N/A	Required
germ_gene_name_hgnc	CodeableConcept	The gene name	HGNC	Required
germ_gene_id_hgnc_id	CodeableConcept	The gene id	HGNC	Required if known
germ_genome_assembly	CodeableConcept	The genome assembly	HGNC	Required if known
germ_cytogen_loc	String	The full cytogenetic location	N/A	Required if known
germ_cytogen_loc_chrom	CodeableConcept	The cytogenetic location (chromosome)	Code Set	Required
germ_cytogen_loc_start_pos	Integer	The cytogenetic location (start position)	N/A	Required
germ_cytogen_loc_end_pos	Integer	The cytogenetic (end position)	N/A	Required
germ_reference_allele	CodeableConcept	Reference Allele (A, T, C, G)	Code Set	Required
germ_altered_allele	CodeableConcept	Altered Allele (A, T, C, G)	Code Set	Required
germ_refseq_id	CodeableConcept	Range(s) of DNA sequence examined	NCBI RefSeq	Required if known
germ_ensembl_id	CodeableConcept	The Ensembl ID	Ensembl	Required if known
germ_mutation_class	CodeableConcept	The mutation classification	Code Set	Required
germ_nucleot_change_hgvs	CodeableConcept	The symbolic representation of a genetic variant reported using HGVS nomenclature (gHGVS)	HGVS	Required
germ_cdna_change_hgvs	String	The change in the coding DNA	N/A	Required
germ_aa_change_hgvs	CodeableConcept	The symbolic representation of an amino acid variant reported using HGVS nomenclature (pHGVS)	HGVS	Required
germ_dbsnp	CodeableConcept	The variation ID assigned by DBSNP	NCBI dbSNP	Required
germ_clinvar	CodeableConcept	The variation ID assigned by ClinVar	NCBI ClinVar	Required
germ_allelic_state	CodeableConcept	The classification of allelic state using one of the five provided codes	LOINC	Required
germline_variant_id	CodeableConcept	The classification of a germline variant according to pathogenicity	LOINC	Required
date_cur_germ_prof_gen	Date	Date of curation	N/A	Required if known
cur_by_germ_prof_gen	String	The name of the curator who modified the instrument	N/A	Required if known

Notes

1. This profile is repeatable and more than one records can be expected per patient
2. The “Code Set” is a custom set of codes defined by the JHU Team