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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: 4-78911552-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=78911552&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "BMP2K",
"hgnc_id": 18041,
"hgvs_c": "c.3005C>G",
"hgvs_p": "p.Thr1002Ser",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_198892.2",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "PAQR3",
"hgnc_id": 30130,
"hgvs_c": "n.*637G>C",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000511594.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 149347,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.128,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"chr": "4",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.001651674509048462,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1161,
"aa_ref": "T",
"aa_start": 1002,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8012,
"cdna_start": 3199,
"cds_end": null,
"cds_length": 3486,
"cds_start": 3005,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_198892.2",
"gene_hgnc_id": 18041,
"gene_symbol": "BMP2K",
"hgvs_c": "c.3005C>G",
"hgvs_p": "p.Thr1002Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000502613.3",
"protein_coding": true,
"protein_id": "NP_942595.1",
"strand": true,
"transcript": "NM_198892.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1161,
"aa_ref": "T",
"aa_start": 1002,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8012,
"cdna_start": 3199,
"cds_end": null,
"cds_length": 3486,
"cds_start": 3005,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000502613.3",
"gene_hgnc_id": 18041,
"gene_symbol": "BMP2K",
"hgvs_c": "c.3005C>G",
"hgvs_p": "p.Thr1002Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_198892.2",
"protein_coding": true,
"protein_id": "ENSP00000424668.2",
"strand": true,
"transcript": "ENST00000502613.3",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2153,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000342820.10",
"gene_hgnc_id": 30130,
"gene_symbol": "PAQR3",
"hgvs_c": "n.*782+3658G>C",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000344203.6",
"strand": false,
"transcript": "ENST00000342820.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1431,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000512760.5",
"gene_hgnc_id": 30130,
"gene_symbol": "PAQR3",
"hgvs_c": "n.*792+3658G>C",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000426875.1",
"strand": false,
"transcript": "ENST00000512760.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1124,
"aa_ref": "T",
"aa_start": 965,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7901,
"cdna_start": 3088,
"cds_end": null,
"cds_length": 3375,
"cds_start": 2894,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_001419799.1",
"gene_hgnc_id": 18041,
"gene_symbol": "BMP2K",
"hgvs_c": "c.2894C>G",
"hgvs_p": "p.Thr965Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001406728.1",
"strand": true,
"transcript": "NM_001419799.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1124,
"aa_ref": "T",
"aa_start": 965,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4384,
"cdna_start": 3076,
"cds_end": null,
"cds_length": 3375,
"cds_start": 2894,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000858772.1",
"gene_hgnc_id": 18041,
"gene_symbol": "BMP2K",
"hgvs_c": "c.2894C>G",
"hgvs_p": "p.Thr965Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528831.1",
"strand": true,
"transcript": "ENST00000858772.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1105,
"aa_ref": "T",
"aa_start": 946,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11667,
"cdna_start": 6854,
"cds_end": null,
"cds_length": 3318,
"cds_start": 2837,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_047415931.1",
"gene_hgnc_id": 18041,
"gene_symbol": "BMP2K",
"hgvs_c": "c.2837C>G",
"hgvs_p": "p.Thr946Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271887.1",
"strand": true,
"transcript": "XM_047415931.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1081,
"aa_ref": "T",
"aa_start": 922,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12450,
"cdna_start": 7637,
"cds_end": null,
"cds_length": 3246,
"cds_start": 2765,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_017008381.2",
"gene_hgnc_id": 18041,
"gene_symbol": "BMP2K",
"hgvs_c": "c.2765C>G",
"hgvs_p": "p.Thr922Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016863870.1",
"strand": true,
"transcript": "XM_017008381.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1081,
"aa_ref": "T",
"aa_start": 922,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8108,
"cdna_start": 3295,
"cds_end": null,
"cds_length": 3246,
"cds_start": 2765,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047415932.1",
"gene_hgnc_id": 18041,
"gene_symbol": "BMP2K",
"hgvs_c": "c.2765C>G",
"hgvs_p": "p.Thr922Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271888.1",
"strand": true,
"transcript": "XM_047415932.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2288,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000511594.5",
"gene_hgnc_id": 30130,
"gene_symbol": "PAQR3",
"hgvs_c": "n.*637G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000425080.1",
"strand": false,
"transcript": "ENST00000511594.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2288,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000511594.5",
"gene_hgnc_id": 30130,
"gene_symbol": "PAQR3",
"hgvs_c": "n.*637G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000425080.1",
"strand": false,
"transcript": "ENST00000511594.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1576,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007096371.1",
"gene_hgnc_id": 30130,
"gene_symbol": "PAQR3",
"hgvs_c": "n.1288+3658G>C",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007096371.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3228,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007096372.1",
"gene_hgnc_id": 30130,
"gene_symbol": "PAQR3",
"hgvs_c": "n.1288+3658G>C",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007096372.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1415,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_938694.4",
"gene_hgnc_id": 30130,
"gene_symbol": "PAQR3",
"hgvs_c": "n.1128-5391G>C",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_938694.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs12507099",
"effect": "missense_variant",
"frequency_reference_population": 0.09253383,
"gene_hgnc_id": 18041,
"gene_symbol": "BMP2K",
"gnomad_exomes_ac": 137243,
"gnomad_exomes_af": 0.0938936,
"gnomad_exomes_homalt": 7524,
"gnomad_genomes_ac": 12104,
"gnomad_genomes_af": 0.079482,
"gnomad_genomes_homalt": 696,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 8220,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.341,
"pos": 78911552,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.2,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_198892.2"
}
]
}