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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: 10-102111121-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=102111121&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP3",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "LDB1",
"hgnc_id": 6532,
"hgvs_c": "c.197A>C",
"hgvs_p": "p.Gln66Pro",
"inheritance_mode": "AD",
"pathogenic_score": 1,
"score": -3,
"transcript": "NM_001113407.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_score": -3,
"allele_count_reference_population": 14,
"alphamissense_prediction": null,
"alphamissense_score": 0.249,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.34,
"chr": "10",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8071882724761963,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 411,
"aa_ref": "Q",
"aa_start": 66,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3098,
"cdna_start": 455,
"cds_end": null,
"cds_length": 1236,
"cds_start": 197,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001113407.3",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.197A>C",
"hgvs_p": "p.Gln66Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000673968.1",
"protein_coding": true,
"protein_id": "NP_001106878.1",
"strand": false,
"transcript": "NM_001113407.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 411,
"aa_ref": "Q",
"aa_start": 66,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3098,
"cdna_start": 455,
"cds_end": null,
"cds_length": 1236,
"cds_start": 197,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000673968.1",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.197A>C",
"hgvs_p": "p.Gln66Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001113407.3",
"protein_coding": true,
"protein_id": "ENSP00000501277.1",
"strand": false,
"transcript": "ENST00000673968.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 375,
"aa_ref": "Q",
"aa_start": 30,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2285,
"cdna_start": 713,
"cds_end": null,
"cds_length": 1128,
"cds_start": 89,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000361198.9",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.89A>C",
"hgvs_p": "p.Gln30Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000354616.5",
"strand": false,
"transcript": "ENST00000361198.9",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 409,
"aa_ref": "Q",
"aa_start": 66,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3092,
"cdna_start": 455,
"cds_end": null,
"cds_length": 1230,
"cds_start": 197,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001321612.2",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.197A>C",
"hgvs_p": "p.Gln66Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308541.1",
"strand": false,
"transcript": "NM_001321612.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 409,
"aa_ref": "Q",
"aa_start": 66,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1938,
"cdna_start": 372,
"cds_end": null,
"cds_length": 1230,
"cds_start": 197,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000425280.2",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.197A>C",
"hgvs_p": "p.Gln66Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000392466.2",
"strand": false,
"transcript": "ENST00000425280.2",
"transcript_support_level": 5
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 375,
"aa_ref": "Q",
"aa_start": 30,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3412,
"cdna_start": 769,
"cds_end": null,
"cds_length": 1128,
"cds_start": 89,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_003893.5",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.89A>C",
"hgvs_p": "p.Gln30Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_003884.1",
"strand": false,
"transcript": "NM_003893.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 375,
"aa_ref": "Q",
"aa_start": 30,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4499,
"cdna_start": 1856,
"cds_end": null,
"cds_length": 1128,
"cds_start": 89,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047425979.1",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.89A>C",
"hgvs_p": "p.Gln30Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047281935.1",
"strand": false,
"transcript": "XM_047425979.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 375,
"aa_ref": "Q",
"aa_start": 30,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2935,
"cdna_start": 292,
"cds_end": null,
"cds_length": 1128,
"cds_start": 89,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047425980.1",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.89A>C",
"hgvs_p": "p.Gln30Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047281936.1",
"strand": false,
"transcript": "XM_047425980.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 339,
"aa_ref": "Q",
"aa_start": 66,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2548,
"cdna_start": 455,
"cds_end": null,
"cds_length": 1020,
"cds_start": 197,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017016867.2",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.197A>C",
"hgvs_p": "p.Gln66Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016872356.1",
"strand": false,
"transcript": "XM_017016867.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 337,
"aa_ref": "Q",
"aa_start": 66,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1287,
"cdna_start": 455,
"cds_end": null,
"cds_length": 1014,
"cds_start": 197,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017016868.2",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.197A>C",
"hgvs_p": "p.Gln66Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016872357.1",
"strand": false,
"transcript": "XM_017016868.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 242,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2494,
"cdna_start": null,
"cds_end": null,
"cds_length": 729,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_017016869.2",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "c.-138A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016872358.1",
"strand": false,
"transcript": "XM_017016869.2",
"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": 478,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000461873.5",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "n.13A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000461873.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2095,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XR_001747255.3",
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"hgvs_c": "n.769A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_001747255.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1463085489",
"effect": "missense_variant",
"frequency_reference_population": 0.000008673833,
"gene_hgnc_id": 6532,
"gene_symbol": "LDB1",
"gnomad_exomes_ac": 10,
"gnomad_exomes_af": 0.0000068405,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262867,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.542,
"pos": 102111121,
"ref": "T",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.392,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001113407.3"
}
]
}