Usually VEP annotates HGVSc notations for any variant that overlaps any transcript. However, when a long deletion or del-ins variant that spans the region outside and within a transcript, it is not generating HGVSc notations. See the following two example variants:
Variant 1:
The following variant overlaps the coding region, 5'UTR and the region outside the transcript of ENST00000304494.5, but it did not get HGVSc. Here the link for the VEP json output for this variant.
CPRA:
9:21974675:ACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCAGCCCCTCCTCTTTCTTCCTCCGGTGCTGGCGGAAGAGCCCCCTCCGACCCTGTCCCTCAAATCCTCTGGAGGGACCGCGGTATCTTTCCAGGCAAGGGGACGCCGTGAGCGAGTGCTCGGAGGAGGTGCTATTAACTCCGAGCACTTAGCGAATGTGGCACCCCTGAAGTCGCCCCAGGTTGGGTCTCCCCCGGGGGCACCAGCCGGAAGCAG:A
HGVSg:
NC_000009.11:g.21974678_21975128del
Variant 2:
The following variant overlaps the coding region, 3'UTR and the region outside the transcript of ENST00000304494.5, but it did not get HGVSc. Here the link for the VEP json output for this variant.
CPRA:
9:21967724:AGGTGCTCAATAAATGTTGACAATAAATGAGTGAATGAATGAAAATTATTTTATTTTTATTTGAGCTTTGGTTCTGCCATTTGCTAGCAGTGTGACTCAAGAGAAGCCAGTAACCCCCCTGAGCTTCCCTAGTTCACAAAATGCTTGTCATGAAGTCGACAGCTTCCGGAGGCTGCGAGGCTCGCAAGAAATGCCCACATGAATGTGCGCTTAGGGCGTGAGTGCTCACTCCAGAAAACTCCAACACAGTGAAAAGGCAGAAGCGGTGTTTTTCTTTTTTACATTTTTATAAGAATATATAAAAAATGATATAAATGGACATTTACGGTAGTGGGGGAAGGCATATATCTACGTTAAAAGGCAGGACATTTTTAAAAGCTCTATTTTCTAAATGAAAACTACGAAAGCGGGGTGGGTTGTGGCGGGGGCAGTTGTGGCCCTGTAGGACCTTCGGTGACTGATGATCTAAGTTTCCCGAGGTTTCTCAGAGCCTCTCTGGTTCTTTCAATCGGG:A
HGVSg:
NC_000009.11:g.21967726_21968237del
Usually VEP annotates HGVSc notations for any variant that overlaps any transcript. However, when a long deletion or del-ins variant that spans the region outside and within a transcript, it is not generating HGVSc notations. See the following two example variants:
Variant 1:
The following variant overlaps the coding region, 5'UTR and the region outside the transcript of ENST00000304494.5, but it did not get HGVSc. Here the link for the VEP json output for this variant.
CPRA:
9:21974675:ACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCAGCCCCTCCTCTTTCTTCCTCCGGTGCTGGCGGAAGAGCCCCCTCCGACCCTGTCCCTCAAATCCTCTGGAGGGACCGCGGTATCTTTCCAGGCAAGGGGACGCCGTGAGCGAGTGCTCGGAGGAGGTGCTATTAACTCCGAGCACTTAGCGAATGTGGCACCCCTGAAGTCGCCCCAGGTTGGGTCTCCCCCGGGGGCACCAGCCGGAAGCAG:AHGVSg:
NC_000009.11:g.21974678_21975128delVariant 2:
The following variant overlaps the coding region, 3'UTR and the region outside the transcript of ENST00000304494.5, but it did not get HGVSc. Here the link for the VEP json output for this variant.
CPRA:
9:21967724:AGGTGCTCAATAAATGTTGACAATAAATGAGTGAATGAATGAAAATTATTTTATTTTTATTTGAGCTTTGGTTCTGCCATTTGCTAGCAGTGTGACTCAAGAGAAGCCAGTAACCCCCCTGAGCTTCCCTAGTTCACAAAATGCTTGTCATGAAGTCGACAGCTTCCGGAGGCTGCGAGGCTCGCAAGAAATGCCCACATGAATGTGCGCTTAGGGCGTGAGTGCTCACTCCAGAAAACTCCAACACAGTGAAAAGGCAGAAGCGGTGTTTTTCTTTTTTACATTTTTATAAGAATATATAAAAAATGATATAAATGGACATTTACGGTAGTGGGGGAAGGCATATATCTACGTTAAAAGGCAGGACATTTTTAAAAGCTCTATTTTCTAAATGAAAACTACGAAAGCGGGGTGGGTTGTGGCGGGGGCAGTTGTGGCCCTGTAGGACCTTCGGTGACTGATGATCTAAGTTTCCCGAGGTTTCTCAGAGCCTCTCTGGTTCTTTCAATCGGG:AHGVSg:
NC_000009.11:g.21967726_21968237del