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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: 4-174508699-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=174508699&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 174508699,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000296522.11",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro",
"transcript": "NM_000860.6",
"protein_id": "NP_000851.2",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 266,
"cds_start": 418,
"cds_end": null,
"cds_length": 801,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 2619,
"mane_select": "ENST00000296522.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro",
"transcript": "ENST00000296522.11",
"protein_id": "ENSP00000296522.6",
"transcript_support_level": 1,
"aa_start": 140,
"aa_end": null,
"aa_length": 266,
"cds_start": 418,
"cds_end": null,
"cds_length": 801,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 2619,
"mane_select": "NM_000860.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro",
"transcript": "ENST00000296521.11",
"protein_id": "ENSP00000296521.7",
"transcript_support_level": 1,
"aa_start": 140,
"aa_end": null,
"aa_length": 178,
"cds_start": 418,
"cds_end": null,
"cds_length": 537,
"cdna_start": 454,
"cdna_end": null,
"cdna_length": 1171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro",
"transcript": "ENST00000542498.5",
"protein_id": "ENSP00000443644.1",
"transcript_support_level": 1,
"aa_start": 140,
"aa_end": null,
"aa_length": 143,
"cds_start": 418,
"cds_end": null,
"cds_length": 432,
"cdna_start": 865,
"cdna_end": null,
"cdna_length": 2786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro",
"transcript": "NM_001145816.3",
"protein_id": "NP_001139288.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 178,
"cds_start": 418,
"cds_end": null,
"cds_length": 537,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 2455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro",
"transcript": "NM_001363574.2",
"protein_id": "NP_001350503.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 176,
"cds_start": 418,
"cds_end": null,
"cds_length": 531,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 1899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro",
"transcript": "ENST00000504433.1",
"protein_id": "ENSP00000420892.1",
"transcript_support_level": 2,
"aa_start": 140,
"aa_end": null,
"aa_length": 176,
"cds_start": 418,
"cds_end": null,
"cds_length": 531,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 1910,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.55G>C",
"hgvs_p": "p.Ala19Pro",
"transcript": "NM_001256301.1",
"protein_id": "NP_001243230.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 145,
"cds_start": 55,
"cds_end": null,
"cds_length": 438,
"cdna_start": 595,
"cdna_end": null,
"cdna_length": 2757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.55G>C",
"hgvs_p": "p.Ala19Pro",
"transcript": "NM_001256307.2",
"protein_id": "NP_001243236.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 145,
"cds_start": 55,
"cds_end": null,
"cds_length": 438,
"cdna_start": 348,
"cdna_end": null,
"cdna_length": 2512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.55G>C",
"hgvs_p": "p.Ala19Pro",
"transcript": "ENST00000510901.5",
"protein_id": "ENSP00000422418.1",
"transcript_support_level": 2,
"aa_start": 19,
"aa_end": null,
"aa_length": 145,
"cds_start": 55,
"cds_end": null,
"cds_length": 438,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 1535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.55G>C",
"hgvs_p": "p.Ala19Pro",
"transcript": "ENST00000541923.5",
"protein_id": "ENSP00000438017.1",
"transcript_support_level": 2,
"aa_start": 19,
"aa_end": null,
"aa_length": 145,
"cds_start": 55,
"cds_end": null,
"cds_length": 438,
"cdna_start": 758,
"cdna_end": null,
"cdna_length": 2920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro",
"transcript": "NM_001256305.2",
"protein_id": "NP_001243234.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 143,
"cds_start": 418,
"cds_end": null,
"cds_length": 432,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 2378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.55G>C",
"hgvs_p": "p.Ala19Pro",
"transcript": "ENST00000506910.5",
"protein_id": "ENSP00000423066.1",
"transcript_support_level": 4,
"aa_start": 19,
"aa_end": null,
"aa_length": 98,
"cds_start": 55,
"cds_end": null,
"cds_length": 298,
"cdna_start": 576,
"cdna_end": null,
"cdna_length": 819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.55G>C",
"hgvs_p": "p.Ala19Pro",
"transcript": "ENST00000514584.5",
"protein_id": "ENSP00000423110.1",
"transcript_support_level": 2,
"aa_start": 19,
"aa_end": null,
"aa_length": 96,
"cds_start": 55,
"cds_end": null,
"cds_length": 291,
"cdna_start": 591,
"cdna_end": null,
"cdna_length": 827,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "n.*47G>C",
"hgvs_p": null,
"transcript": "ENST00000508330.5",
"protein_id": "ENSP00000425741.1",
"transcript_support_level": 2,
"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": 1046,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "n.*180G>C",
"hgvs_p": null,
"transcript": "ENST00000510835.5",
"protein_id": "ENSP00000427699.1",
"transcript_support_level": 5,
"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": 1553,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "n.399G>C",
"hgvs_p": null,
"transcript": "ENST00000512410.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 666,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "n.455G>C",
"hgvs_p": null,
"transcript": "XR_938728.3",
"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": 1222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "n.*47G>C",
"hgvs_p": null,
"transcript": "ENST00000508330.5",
"protein_id": "ENSP00000425741.1",
"transcript_support_level": 2,
"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": 1046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "n.*180G>C",
"hgvs_p": null,
"transcript": "ENST00000510835.5",
"protein_id": "ENSP00000427699.1",
"transcript_support_level": 5,
"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": 1553,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.218-13075G>C",
"hgvs_p": null,
"transcript": "NM_001256306.2",
"protein_id": "NP_001243235.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2415,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"hgvs_c": "c.218-13075G>C",
"hgvs_p": null,
"transcript": "ENST00000422112.6",
"protein_id": "ENSP00000398720.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HPGD",
"gene_hgnc_id": 5154,
"dbsnp": "rs121434480",
"frequency_reference_population": 0.000027841053,
"hom_count_reference_population": 0,
"allele_count_reference_population": 44,
"gnomad_exomes_af": 0.0000294049,
"gnomad_genomes_af": 0.000013152,
"gnomad_exomes_ac": 42,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9720017910003662,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.835,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9709,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.808,
"phylop100way_prediction": "Uncertain_significance",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000296522.11",
"gene_symbol": "HPGD",
"hgnc_id": 5154,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown,AD",
"hgvs_c": "c.418G>C",
"hgvs_p": "p.Ala140Pro"
}
],
"clinvar_disease": " 1, autosomal recessive, primary,Cranioosteoarthropathy,Hypertrophic osteoarthropathy,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Cranioosteoarthropathy|Hypertrophic osteoarthropathy, primary, autosomal recessive, 1|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}