PhyloP Question- Different on UCSC browser

General
1

Hi,

I am researching chr7-138752654 G>A [hg38] and looking into in silico scores. On gnomAD it shows PhyloP of 4.93, PolyPhen ~.8.

On UCSC it shows PhyloP score of ~.8

Can you please explain the discrepancy? See below for links. Thank you!

  1. gnomAD: https://gnomad.broadinstitute.org/variant/7-138752654-G-A?dataset=gnomad_r4

  2. UCSC: https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr7%3A138752654%2D138752654&hgsid=2301997578_dNjfeGLha3JWhaesovFeABikjl1O

2

Hi @tnd35,

gnomAD v4 used the 241 mammalian PhyloP scores. The link you provided shows UCSC defaulting to the 100 vertebrate track. Loading the 241 track, “Basewise Cons”, will result in both browsers showing the same score.

Best,
Mike