If you are looking for any metafields at the variant level then you need to iterate through products, and then drill into the variants to get to them. Like this stripped-down example below. I just pull the first 5 products, iterate through each product’s first 5 variants, and finally iterate through each variant’s first 5 metafields. Does this work for you?
{
products(first: 5) {
edges {
node {
id
title
variants(first: 5) {
edges {
node {
id
title
metafields(first: 5) {
edges {
node {
description
value
valueType
}
}
}
}
}
}
}
}
}
}