fix: solve NULLs found in variantEffect struct of the variant index

[vivienho]

✨ Context

In the variant index, NULLs were found in the variantEffect struct.

-RECORD 0--------------------------------------------------------------------------------------------------------------------------------------
 variantId     | 11_51584799_A_C                                                                                                               
 variantEffect | [{VEP, intergenic_variant, 0.0, NULL, NULL, 0.0}, {NULL, NULL, NULL, NULL, NULL, NULL}, {NULL, NULL, NULL, NULL, NULL, NULL}] 

This is because variant effect assessments other than VEP are not available for intergenic variants.

🛠 What does this PR implement

• In these cases, we only extract the VEP prediction for the variantEffect struct but not the other variant effect assessments.
• The vep output schema (the intergenic_consequences struct) is incorrect. This PR removes the incorrect fields.

🙈 Missing

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[DSuveges]

When no transcript consequences were available, we were expecting in silico predictors being available in the intergenic_consequences field. This was an unfounded assumption leading to all null variant annotations. This PR sorts this out.

However, predictors unrelated to transcripts eg. conservation, cadd should be available even if the consequence of the variant is intergenic.