← Back to variant description
GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 19-49862186-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49862186&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49862186,
"ref": "C",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_007254.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly",
"transcript": "NM_007254.4",
"protein_id": "NP_009185.2",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 521,
"cds_start": 1125,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000322344.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007254.4"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly",
"transcript": "ENST00000322344.8",
"protein_id": "ENSP00000323511.2",
"transcript_support_level": 1,
"aa_start": 375,
"aa_end": null,
"aa_length": 521,
"cds_start": 1125,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007254.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000322344.8"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly",
"transcript": "ENST00000596014.5",
"protein_id": "ENSP00000472300.1",
"transcript_support_level": 1,
"aa_start": 375,
"aa_end": null,
"aa_length": 521,
"cds_start": 1125,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596014.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*1052G>T",
"hgvs_p": null,
"transcript": "ENST00000593946.5",
"protein_id": "ENSP00000468896.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000593946.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*1052G>T",
"hgvs_p": null,
"transcript": "ENST00000593946.5",
"protein_id": "ENSP00000468896.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000593946.5"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1152G>T",
"hgvs_p": "p.Gly384Gly",
"transcript": "ENST00000861313.1",
"protein_id": "ENSP00000531372.1",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 530,
"cds_start": 1152,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861313.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1152G>T",
"hgvs_p": "p.Gly384Gly",
"transcript": "ENST00000934451.1",
"protein_id": "ENSP00000604510.1",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 530,
"cds_start": 1152,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934451.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly",
"transcript": "ENST00000934445.1",
"protein_id": "ENSP00000604504.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 521,
"cds_start": 1125,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934445.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly",
"transcript": "ENST00000934450.1",
"protein_id": "ENSP00000604509.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 521,
"cds_start": 1125,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934450.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1104G>T",
"hgvs_p": "p.Gly368Gly",
"transcript": "ENST00000934449.1",
"protein_id": "ENSP00000604508.1",
"transcript_support_level": null,
"aa_start": 368,
"aa_end": null,
"aa_length": 514,
"cds_start": 1104,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934449.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1092G>T",
"hgvs_p": "p.Gly364Gly",
"transcript": "ENST00000965095.1",
"protein_id": "ENSP00000635154.1",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 510,
"cds_start": 1092,
"cds_end": null,
"cds_length": 1533,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965095.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1086G>T",
"hgvs_p": "p.Gly362Gly",
"transcript": "ENST00000934448.1",
"protein_id": "ENSP00000604507.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 508,
"cds_start": 1086,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934448.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1083G>T",
"hgvs_p": "p.Gly361Gly",
"transcript": "ENST00000861311.1",
"protein_id": "ENSP00000531370.1",
"transcript_support_level": null,
"aa_start": 361,
"aa_end": null,
"aa_length": 507,
"cds_start": 1083,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861311.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1032G>T",
"hgvs_p": "p.Gly344Gly",
"transcript": "ENST00000600573.5",
"protein_id": "ENSP00000469826.1",
"transcript_support_level": 5,
"aa_start": 344,
"aa_end": null,
"aa_length": 490,
"cds_start": 1032,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600573.5"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1017G>T",
"hgvs_p": "p.Gly339Gly",
"transcript": "ENST00000631020.2",
"protein_id": "ENSP00000486707.1",
"transcript_support_level": 5,
"aa_start": 339,
"aa_end": null,
"aa_length": 485,
"cds_start": 1017,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000631020.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.999G>T",
"hgvs_p": "p.Gly333Gly",
"transcript": "ENST00000861312.1",
"protein_id": "ENSP00000531371.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 479,
"cds_start": 999,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861312.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.999G>T",
"hgvs_p": "p.Gly333Gly",
"transcript": "ENST00000965096.1",
"protein_id": "ENSP00000635155.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 479,
"cds_start": 999,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965096.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.978G>T",
"hgvs_p": "p.Gly326Gly",
"transcript": "ENST00000965094.1",
"protein_id": "ENSP00000635153.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 472,
"cds_start": 978,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965094.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly",
"transcript": "ENST00000934444.1",
"protein_id": "ENSP00000604503.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 471,
"cds_start": 1125,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934444.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly",
"transcript": "ENST00000600910.5",
"protein_id": "ENSP00000473137.1",
"transcript_support_level": 5,
"aa_start": 375,
"aa_end": null,
"aa_length": 455,
"cds_start": 1125,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600910.5"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly",
"transcript": "ENST00000934447.1",
"protein_id": "ENSP00000604506.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 455,
"cds_start": 1125,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934447.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.894G>T",
"hgvs_p": "p.Gly298Gly",
"transcript": "ENST00000934446.1",
"protein_id": "ENSP00000604505.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 444,
"cds_start": 894,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934446.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.825G>T",
"hgvs_p": "p.Gly275Gly",
"transcript": "ENST00000934452.1",
"protein_id": "ENSP00000604511.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 421,
"cds_start": 825,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934452.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.744G>T",
"hgvs_p": "p.Gly248Gly",
"transcript": "ENST00000627317.1",
"protein_id": "ENSP00000486500.1",
"transcript_support_level": 5,
"aa_start": 248,
"aa_end": null,
"aa_length": 254,
"cds_start": 744,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000627317.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.480G>T",
"hgvs_p": null,
"transcript": "ENST00000593706.3",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000593706.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.1626G>T",
"hgvs_p": null,
"transcript": "ENST00000594661.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000594661.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.24G>T",
"hgvs_p": null,
"transcript": "ENST00000601816.3",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000601816.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*520G>T",
"hgvs_p": null,
"transcript": "ENST00000627232.2",
"protein_id": "ENSP00000486037.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000627232.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*520G>T",
"hgvs_p": null,
"transcript": "ENST00000627232.2",
"protein_id": "ENSP00000486037.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000627232.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.208-81G>T",
"hgvs_p": null,
"transcript": "ENST00000625216.2",
"protein_id": "ENSP00000486898.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000625216.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.-111G>T",
"hgvs_p": null,
"transcript": "ENST00000599454.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000599454.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*85G>T",
"hgvs_p": null,
"transcript": "ENST00000629179.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000629179.1"
}
],
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"dbsnp": "rs727504101",
"frequency_reference_population": 0.000006157964,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000615796,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5400000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.00800000037997961,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.49,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000872604383729988,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_007254.4",
"gene_symbol": "PNKP",
"hgnc_id": 9154,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1125G>T",
"hgvs_p": "p.Gly375Gly"
}
],
"clinvar_disease": " 12,Developmental and epileptic encephalopathy",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Developmental and epileptic encephalopathy, 12",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}