29af14b47208040441ab4ff7acf51aac71cad4e2
lrnassar
  Thu Sep 17 21:58:18 2026 -0700
Adding MaveMD track, clinically calibrated multiplexed variant effect measurements on hg38. refs #37800

MaveMD is a curated collection inside MaveDB holding the score sets with clinical
relevance, restricted to genes with a moderate or stronger gene-disease association.
Data come from the MaveDB API rather than the Zenodo snapshots, at the request of the
MaveDB team, who also set the request pacing the fetch script follows.

Two views under a new phenDis container. mavemdVar draws one item per measured variant
per score set, carrying the assay score, the functional class, the ACMG/AMP functional
evidence code and strength where the score set is calibrated, the assay metadata, and
matching ClinVar and gnomAD annotations. mavemdMap draws each score set as a variant
effect map, one column per amino acid position and one row per substitution, reusing
Jonathan's heatmap display from the MaveDB track.

MaveDB resolves about a third of the collection to the genome and the rest only to a
protein sequence, so variants are placed from the genomic HGVS term where one exists,
otherwise by projecting the protein term onto its codon through ncbiRefSeqLink and
ncbiRefSeqCurated for RefSeq accessions or the GENCODE tables for Ensembl ones,
otherwise by running the submitted transcript term through hgvsToVcf. The projection is
cross-checked against the variants carrying both coordinate systems and the build aborts
if they disagree beyond a threshold. Codons split across an exon junction are written as
BED12 with the two real blocks. Haplotypes cannot be given a single position and are
excluded, with every dropped measurement counted by reason in the makeDoc.

Also adds reciprocal relatedTracks entries between mavedb and mavemd. Gated alpha
pending QA.

diff --git src/hg/makeDb/scripts/mavemd/mavemdVariants.as src/hg/makeDb/scripts/mavemd/mavemdVariants.as
new file mode 100644
index 00000000000..830805405d4
--- /dev/null
+++ src/hg/makeDb/scripts/mavemd/mavemdVariants.as
@@ -0,0 +1,50 @@
+table mavemdVariants
+"MaveMD variant effect measurements with ACMG functional evidence"
+    (
+    string chrom;          "Chromosome"
+    uint   chromStart;     "Start position in chromosome"
+    uint   chromEnd;       "End position in chromosome"
+    string name;           "Gene and amino acid change"
+    uint   score;          "Score 0-1000 (ACMG evidence strength)"
+    char[1] strand;        "Strand|Transcript strand for codon-projected items; . where the variant was placed from a genomic term"
+    uint   thickStart;     "Start of thick display"
+    uint   thickEnd;       "End of thick display"
+    uint   reserved;       "Item color (RGB)"
+    int    blockCount;     "Number of blocks"
+    int[blockCount] blockSizes;  "Block sizes"
+    int[blockCount] chromStarts; "Block starts relative to chromStart"
+    string gene;           "Gene"
+    string proteinChange;  "Protein change"
+    string acmgOutcome;    "ACMG evidence|Evidence code from the displayed calibration"
+    string acmgStrength;   "Evidence strength"
+    string funcClass;      "Functional class|Measured effect: normal, abnormal or indeterminate"
+    string funcScore;      "Functional score|Assay score, on this score set's own scale"
+    string oddsPath;       "OddsPath|Odds of pathogenicity for this functional class"
+    string calibration;    "Calibration|The calibration whose call is shown"
+    string calibrationSource; "Calibration chosen by|How the displayed calibration was picked"
+    string researchUseOnly; "Research use only|Whether the displayed calibration is marked research use only"
+    lstring allCalibrations; "All calibrations|Every calibration on this score set and its call"
+    string clinvarSig;     "ClinVar significance"
+    string clinvarReview;  "ClinVar review status"
+    string clinvarRelease; "ClinVar release|Which ClinVar snapshot this classification came from"
+    string gnomadAf;       "gnomAD allele frequency"
+    string gnomadAc;       "gnomAD allele count"
+    string gnomadAn;       "gnomAD allele number"
+    string gnomadFaf95;    "gnomAD FAF95|Filtering allele frequency, 95% confidence"
+    string gnomadFaf95Ancestry; "gnomAD FAF95 ancestry|Ancestry group giving the filtering allele frequency"
+    string gnomadVersion;  "gnomAD version"
+    string vepConsequence; "VEP consequence|Empty throughout at present; carried so the track picks up MaveDB's values if they are populated"
+    string scoreSet;       "Score set"
+    lstring scoreSetTitle; "Score set title"
+    string assayMethod;    "Assay method|What the assay measured"
+    string assayModel;     "Assay model system"
+    lstring assayMechanism; "Molecular mechanism assessed"
+    string libraryMethod;  "Variant library method|An in vitro construct library cannot detect effects on splicing or nonsense-mediated decay"
+    lstring publication;   "Publication"
+    lstring publicationUrl; "Publication link"
+    string genomicChange;  "Genomic HGVS"
+    string cdnaChange;     "cDNA HGVS"
+    string clinGenId;      "ClinGen allele ID|CA = canonical (genomic) allele, PA = protein allele"
+    string variantUrn;     "MaveDB variant"
+    string placement;      "Placement method|How this variant was placed on the genome"
+    )