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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: 19-501900-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=501900&ref=C&alt=A&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": "MADCAM1",
"hgnc_id": 6765,
"hgvs_c": "c.899C>A",
"hgvs_p": "p.Pro300His",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_130760.3",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MADCAM1-AS1",
"hgnc_id": 55315,
"hgvs_c": "n.154-276G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000813738.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 328301,
"alphamissense_prediction": null,
"alphamissense_score": 0.1052,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.66,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0029996633529663086,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 382,
"aa_ref": "P",
"aa_start": 300,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1541,
"cdna_start": 913,
"cds_end": null,
"cds_length": 1149,
"cds_start": 899,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_130760.3",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.899C>A",
"hgvs_p": "p.Pro300His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000215637.8",
"protein_coding": true,
"protein_id": "NP_570116.2",
"strand": true,
"transcript": "NM_130760.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 382,
"aa_ref": "P",
"aa_start": 300,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1541,
"cdna_start": 913,
"cds_end": null,
"cds_length": 1149,
"cds_start": 899,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000215637.8",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.899C>A",
"hgvs_p": "p.Pro300His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_130760.3",
"protein_coding": true,
"protein_id": "ENSP00000215637.2",
"strand": true,
"transcript": "ENST00000215637.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 295,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1309,
"cdna_start": null,
"cds_end": null,
"cds_length": 888,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000346144.8",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.668-2845C>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000304247.2",
"strand": true,
"transcript": "ENST00000346144.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 200,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 603,
"cdna_start": null,
"cds_end": null,
"cds_length": 603,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000382683.8",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.383-2845C>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000372130.4",
"strand": true,
"transcript": "ENST00000382683.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 429,
"aa_ref": "P",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1673,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 1290,
"cds_start": 1040,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000949592.1",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.1040C>A",
"hgvs_p": "p.Pro347His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619651.1",
"strand": true,
"transcript": "ENST00000949592.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 287,
"aa_ref": "P",
"aa_start": 205,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1250,
"cdna_start": 631,
"cds_end": null,
"cds_length": 864,
"cds_start": 614,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000868303.1",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.614C>A",
"hgvs_p": "p.Pro205His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538362.1",
"strand": true,
"transcript": "ENST00000868303.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 163,
"aa_ref": "P",
"aa_start": 81,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1723,
"cdna_start": 1096,
"cds_end": null,
"cds_length": 492,
"cds_start": 242,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000587541.5",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.242C>A",
"hgvs_p": "p.Pro81His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000475575.1",
"strand": true,
"transcript": "ENST00000587541.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 295,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1280,
"cdna_start": null,
"cds_end": null,
"cds_length": 888,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_130762.3",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.668-2845C>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_570118.1",
"strand": true,
"transcript": "NM_130762.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1247,
"cdna_start": null,
"cds_end": null,
"cds_length": 858,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000949591.1",
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"hgvs_c": "c.638-2845C>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619650.1",
"strand": true,
"transcript": "ENST00000949591.1",
"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": 850,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000592413.2",
"gene_hgnc_id": 55315,
"gene_symbol": "MADCAM1-AS1",
"hgvs_c": "n.459-276G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000592413.2",
"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": 1306,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000813738.1",
"gene_hgnc_id": 55315,
"gene_symbol": "MADCAM1-AS1",
"hgvs_c": "n.154-276G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000813738.1",
"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": 2370,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007067073.1",
"gene_hgnc_id": 55315,
"gene_symbol": "MADCAM1-AS1",
"hgvs_c": "n.515-276G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007067073.1",
"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": 690,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_936221.4",
"gene_hgnc_id": 55315,
"gene_symbol": "MADCAM1-AS1",
"hgvs_c": "n.515-276G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_936221.4",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs3745925",
"effect": "missense_variant",
"frequency_reference_population": 0.21244581,
"gene_hgnc_id": 6765,
"gene_symbol": "MADCAM1",
"gnomad_exomes_ac": 295833,
"gnomad_exomes_af": 0.212303,
"gnomad_exomes_homalt": 32107,
"gnomad_genomes_ac": 32468,
"gnomad_genomes_af": 0.213757,
"gnomad_genomes_homalt": 3561,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 35668,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.031,
"pos": 501900,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.155,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_130760.3"
}
]
}