f30798ae5d11e88e0ab7eb2bcab634e253fd0675
max
  Thu Apr 23 10:36:40 2026 -0700
Add gnomAD MPC v4.1.1 track to hg38.

New composite track under the gnomAD container showing per-variant
MPC (Missense deleteriousness Prediction by Constraint) scores from
gnomAD v4.1.1. Four bigWigs provide per-base scores (one per ALT
nucleotide); a companion bigBed carries the ~250K multi-transcript
variants with a per-transcript breakdown. Included via 'alpha' for
QA review. refs #37434

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/hg38/gnomadMpc.ra src/hg/makeDb/trackDb/human/hg38/gnomadMpc.ra
new file mode 100644
index 00000000000..22bd87b4860
--- /dev/null
+++ src/hg/makeDb/trackDb/human/hg38/gnomadMpc.ra
@@ -0,0 +1,79 @@
+track gnomadMpc
+parent gnomadVariants
+compositeTrack on
+shortLabel gnomAD MPC
+longLabel gnomAD Missense Badness, PolyPhen-2, and Constraint (MPC) v4.1.1
+type bigWig
+visibility hide
+group varRep
+maxWindowToDraw 10000000
+mouseOverFunction noAverage
+dataVersion Release v4.1.1 (2026-02-10)
+html gnomadMpc
+
+    track gnomadMpcA
+    parent gnomadMpc on
+    shortLabel MPC alt=A
+    longLabel gnomAD MPC score: alt allele is A
+    type bigWig
+    visibility dense
+    bigDataUrl /gbdb/hg38/gnomAD/mpc/a.bw
+    maxHeightPixels 128:20:8
+    viewLimits 0:3
+    viewLimitsMax 0:6
+    color 68,1,84
+
+    track gnomadMpcC
+    parent gnomadMpc on
+    shortLabel MPC alt=C
+    longLabel gnomAD MPC score: alt allele is C
+    type bigWig
+    visibility dense
+    bigDataUrl /gbdb/hg38/gnomAD/mpc/c.bw
+    maxHeightPixels 128:20:8
+    viewLimits 0:3
+    viewLimitsMax 0:6
+    color 59,82,139
+
+    track gnomadMpcG
+    parent gnomadMpc on
+    shortLabel MPC alt=G
+    longLabel gnomAD MPC score: alt allele is G
+    type bigWig
+    visibility dense
+    bigDataUrl /gbdb/hg38/gnomAD/mpc/g.bw
+    maxHeightPixels 128:20:8
+    viewLimits 0:3
+    viewLimitsMax 0:6
+    color 33,144,141
+
+    track gnomadMpcT
+    parent gnomadMpc on
+    shortLabel MPC alt=T
+    longLabel gnomAD MPC score: alt allele is T
+    type bigWig
+    visibility dense
+    bigDataUrl /gbdb/hg38/gnomAD/mpc/t.bw
+    maxHeightPixels 128:20:8
+    viewLimits 0:3
+    viewLimitsMax 0:6
+    color 253,231,36
+
+track gnomadMpcOverlaps
+parent gnomadVariants
+shortLabel gnomAD MPC overlaps
+longLabel gnomAD MPC v4.1.1 - variants scored against multiple transcripts
+type bigBed 9 +
+itemRgb on
+visibility hide
+group varRep
+bigDataUrl /gbdb/hg38/gnomAD/mpc/mpcOverlaps.bb
+dataVersion Release v4.1.1 (2026-02-10)
+labelFields name
+skipFields transcripts,mpcByTranscript
+filter.mpcMax 0:6
+filterByRange.mpcMax on
+filterLimits.mpcMax 0:6
+filterLabel.mpcMax Filter by max MPC score
+mouseOver <b>$ref&gt;$alt</b>, max MPC = $mpcMax across $nTranscripts transcripts
+html gnomadMpc