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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: 16-66549940-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=66549940&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 66549940,
"ref": "G",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000544898.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His",
"transcript": "NM_004614.5",
"protein_id": "NP_004605.4",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 265,
"cds_start": 122,
"cds_end": null,
"cds_length": 798,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 4824,
"mane_select": "ENST00000544898.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His",
"transcript": "ENST00000544898.6",
"protein_id": "ENSP00000440898.2",
"transcript_support_level": 1,
"aa_start": 41,
"aa_end": null,
"aa_length": 265,
"cds_start": 122,
"cds_end": null,
"cds_length": 798,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 4824,
"mane_select": "NM_004614.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.65C>A",
"hgvs_p": "p.Pro22His",
"transcript": "ENST00000527284.6",
"protein_id": "ENSP00000435312.2",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 219,
"cds_start": 65,
"cds_end": null,
"cds_length": 660,
"cdna_start": 66,
"cdna_end": null,
"cdna_length": 1822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "n.122C>A",
"hgvs_p": null,
"transcript": "ENST00000567357.6",
"protein_id": "ENSP00000457959.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2266,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.31+313C>A",
"hgvs_p": null,
"transcript": "ENST00000451102.7",
"protein_id": "ENSP00000414334.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 234,
"cds_start": -4,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.31+313C>A",
"hgvs_p": null,
"transcript": "ENST00000299697.12",
"protein_id": "ENSP00000299697.9",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 209,
"cds_start": -4,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.31+313C>A",
"hgvs_p": null,
"transcript": "ENST00000569718.6",
"protein_id": "ENSP00000464313.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 146,
"cds_start": -4,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His",
"transcript": "ENST00000564917.5",
"protein_id": "ENSP00000455187.1",
"transcript_support_level": 3,
"aa_start": 41,
"aa_end": null,
"aa_length": 282,
"cds_start": 122,
"cds_end": null,
"cds_length": 849,
"cdna_start": 167,
"cdna_end": null,
"cdna_length": 1156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His",
"transcript": "NM_001172645.2",
"protein_id": "NP_001166116.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 247,
"cds_start": 122,
"cds_end": null,
"cds_length": 744,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 4770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His",
"transcript": "ENST00000417693.8",
"protein_id": "ENSP00000407469.5",
"transcript_support_level": 2,
"aa_start": 41,
"aa_end": null,
"aa_length": 247,
"cds_start": 122,
"cds_end": null,
"cds_length": 744,
"cdna_start": 251,
"cdna_end": null,
"cdna_length": 1046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His",
"transcript": "NM_001172644.2",
"protein_id": "NP_001166115.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 240,
"cds_start": 122,
"cds_end": null,
"cds_length": 723,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 4749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His",
"transcript": "ENST00000545043.6",
"protein_id": "ENSP00000438143.2",
"transcript_support_level": 2,
"aa_start": 41,
"aa_end": null,
"aa_length": 240,
"cds_start": 122,
"cds_end": null,
"cds_length": 723,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 1120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.-121C>A",
"hgvs_p": null,
"transcript": "NM_001271934.2",
"protein_id": "NP_001258863.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 216,
"cds_start": -4,
"cds_end": null,
"cds_length": 651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His",
"transcript": "ENST00000620035.5",
"protein_id": "ENSP00000483833.2",
"transcript_support_level": 2,
"aa_start": 41,
"aa_end": null,
"aa_length": 152,
"cds_start": 122,
"cds_end": null,
"cds_length": 459,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 3140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000261519",
"gene_hgnc_id": null,
"hgvs_c": "n.661G>T",
"hgvs_p": null,
"transcript": "ENST00000563151.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1910,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "n.165C>A",
"hgvs_p": null,
"transcript": "ENST00000679327.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "n.183C>A",
"hgvs_p": null,
"transcript": "NR_073520.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.-121C>A",
"hgvs_p": null,
"transcript": "NM_001271934.2",
"protein_id": "NP_001258863.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 216,
"cds_start": -4,
"cds_end": null,
"cds_length": 651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.-531C>A",
"hgvs_p": null,
"transcript": "NM_001272050.2",
"protein_id": "NP_001258979.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": -4,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.-1044C>A",
"hgvs_p": null,
"transcript": "ENST00000677420.1",
"protein_id": "ENSP00000504648.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": -4,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.31+313C>A",
"hgvs_p": null,
"transcript": "NM_001172643.1",
"protein_id": "NP_001166114.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 234,
"cds_start": -4,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.-167-931C>A",
"hgvs_p": null,
"transcript": "ENST00000678015.1",
"protein_id": "ENSP00000502959.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": -4,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TK2",
"gene_hgnc_id": 11831,
"hgvs_c": "c.-92-931C>A",
"hgvs_p": null,
"transcript": "ENST00000678297.1",
"protein_id": "ENSP00000503472.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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{
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},
{
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}
],
"gene_symbol": "TK2",
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"dbsnp": "rs201904720",
"frequency_reference_population": 0.0007141781,
"hom_count_reference_population": 4,
"allele_count_reference_population": 967,
"gnomad_exomes_af": 0.000697337,
"gnomad_genomes_af": 0.000847068,
"gnomad_exomes_ac": 838,
"gnomad_genomes_ac": 129,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007720589637756348,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.0860000029206276,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.371,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0927,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 0.16,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000281461854450436,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000544898.6",
"gene_symbol": "TK2",
"hgnc_id": 11831,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.122C>A",
"hgvs_p": "p.Pro41His"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000563151.1",
"gene_symbol": "ENSG00000261519",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.661G>T",
"hgvs_p": null
}
],
"clinvar_disease": " myopathic form,Mitochondrial DNA depletion syndrome,TK2-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:1",
"phenotype_combined": "Mitochondrial DNA depletion syndrome, myopathic form|not provided|TK2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}