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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: 5-56916898-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=56916898&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 56916898,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_153706.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.896G>T",
"hgvs_p": "p.Ser299Ile",
"transcript": "NM_153706.4",
"protein_id": "NP_714917.2",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 299,
"cds_start": 896,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000285947.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153706.4"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.896G>T",
"hgvs_p": "p.Ser299Ile",
"transcript": "ENST00000285947.5",
"protein_id": "ENSP00000285947.2",
"transcript_support_level": 1,
"aa_start": 299,
"aa_end": null,
"aa_length": 299,
"cds_start": 896,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_153706.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000285947.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.812+1932G>T",
"hgvs_p": null,
"transcript": "ENST00000628593.1",
"protein_id": "ENSP00000486609.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 271,
"cds_start": null,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000628593.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.863G>T",
"hgvs_p": "p.Ser288Ile",
"transcript": "ENST00000918990.1",
"protein_id": "ENSP00000589049.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 288,
"cds_start": 863,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918990.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.818G>T",
"hgvs_p": "p.Ser273Ile",
"transcript": "NM_001323018.2",
"protein_id": "NP_001309947.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 273,
"cds_start": 818,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001323018.2"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.674G>T",
"hgvs_p": "p.Ser225Ile",
"transcript": "ENST00000918991.1",
"protein_id": "ENSP00000589050.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 225,
"cds_start": 674,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918991.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.464G>T",
"hgvs_p": "p.Ser155Ile",
"transcript": "ENST00000886482.1",
"protein_id": "ENSP00000556541.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 155,
"cds_start": 464,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886482.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.440G>T",
"hgvs_p": "p.Ser147Ile",
"transcript": "NM_001323022.1",
"protein_id": "NP_001309951.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 147,
"cds_start": 440,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001323022.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.431G>T",
"hgvs_p": "p.Ser144Ile",
"transcript": "ENST00000886483.1",
"protein_id": "ENSP00000556542.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 144,
"cds_start": 431,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886483.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.404G>T",
"hgvs_p": "p.Ser135Ile",
"transcript": "ENST00000941154.1",
"protein_id": "ENSP00000611213.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 135,
"cds_start": 404,
"cds_end": null,
"cds_length": 408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941154.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.242G>T",
"hgvs_p": "p.Ser81Ile",
"transcript": "ENST00000918989.1",
"protein_id": "ENSP00000589048.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 81,
"cds_start": 242,
"cds_end": null,
"cds_length": 246,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918989.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.800G>T",
"hgvs_p": "p.Ser267Ile",
"transcript": "XM_011543139.3",
"protein_id": "XP_011541441.1",
"transcript_support_level": null,
"aa_start": 267,
"aa_end": null,
"aa_length": 267,
"cds_start": 800,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011543139.3"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.668G>T",
"hgvs_p": "p.Ser223Ile",
"transcript": "XM_011543140.4",
"protein_id": "XP_011541442.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 223,
"cds_start": 668,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011543140.4"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.464G>T",
"hgvs_p": "p.Ser155Ile",
"transcript": "XM_005248426.5",
"protein_id": "XP_005248483.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 155,
"cds_start": 464,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005248426.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "c.812+1932G>T",
"hgvs_p": null,
"transcript": "NM_001171990.3",
"protein_id": "NP_001165461.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 271,
"cds_start": null,
"cds_end": null,
"cds_length": 816,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001171990.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "n.*408G>T",
"hgvs_p": null,
"transcript": "ENST00000418299.5",
"protein_id": "ENSP00000398449.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000418299.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "n.765G>T",
"hgvs_p": null,
"transcript": "ENST00000463805.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000463805.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "n.859G>T",
"hgvs_p": null,
"transcript": "ENST00000475908.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000475908.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "n.578G>T",
"hgvs_p": null,
"transcript": "NR_136556.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_136556.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "n.763G>T",
"hgvs_p": null,
"transcript": "NR_136557.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_136557.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "n.*408G>T",
"hgvs_p": null,
"transcript": "ENST00000418299.5",
"protein_id": "ENSP00000398449.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000418299.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"hgvs_c": "n.494+1932G>T",
"hgvs_p": null,
"transcript": "NR_136555.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_136555.2"
}
],
"gene_symbol": "SETD9",
"gene_hgnc_id": 28508,
"dbsnp": "rs746822110",
"frequency_reference_population": 0.0000013846752,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000138468,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.17704156041145325,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.03,
"revel_prediction": "Benign",
"alphamissense_score": 0.5714,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.911,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_153706.4",
"gene_symbol": "SETD9",
"hgnc_id": 28508,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.896G>T",
"hgvs_p": "p.Ser299Ile"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}