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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: 21-44890171-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=44890171&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 44890171,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000652462.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1464G>A",
"hgvs_p": "p.Arg488Arg",
"transcript": "NM_000211.5",
"protein_id": "NP_000202.3",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 769,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1546,
"cdna_end": null,
"cdna_length": 2807,
"mane_select": "ENST00000652462.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1464G>A",
"hgvs_p": "p.Arg488Arg",
"transcript": "ENST00000652462.1",
"protein_id": "ENSP00000498780.1",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 769,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1546,
"cdna_end": null,
"cdna_length": 2807,
"mane_select": "NM_000211.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1536G>A",
"hgvs_p": "p.Arg512Arg",
"transcript": "ENST00000302347.10",
"protein_id": "ENSP00000303242.6",
"transcript_support_level": 1,
"aa_start": 512,
"aa_end": null,
"aa_length": 793,
"cds_start": 1536,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 1618,
"cdna_end": null,
"cdna_length": 2867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1464G>A",
"hgvs_p": "p.Arg488Arg",
"transcript": "ENST00000397852.5",
"protein_id": "ENSP00000380950.1",
"transcript_support_level": 1,
"aa_start": 488,
"aa_end": null,
"aa_length": 769,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1508,
"cdna_end": null,
"cdna_length": 2769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1293G>A",
"hgvs_p": "p.Arg431Arg",
"transcript": "ENST00000397854.7",
"protein_id": "ENSP00000380952.3",
"transcript_support_level": 1,
"aa_start": 431,
"aa_end": null,
"aa_length": 712,
"cds_start": 1293,
"cds_end": null,
"cds_length": 2139,
"cdna_start": 1331,
"cdna_end": null,
"cdna_length": 2592,
"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": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "n.3520G>A",
"hgvs_p": null,
"transcript": "ENST00000498666.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 4781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1464G>A",
"hgvs_p": "p.Arg488Arg",
"transcript": "NM_001127491.3",
"protein_id": "NP_001120963.2",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 769,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1629,
"cdna_end": null,
"cdna_length": 2890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1464G>A",
"hgvs_p": "p.Arg488Arg",
"transcript": "ENST00000355153.8",
"protein_id": "ENSP00000347279.4",
"transcript_support_level": 2,
"aa_start": 488,
"aa_end": null,
"aa_length": 769,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1652,
"cdna_end": null,
"cdna_length": 2913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1464G>A",
"hgvs_p": "p.Arg488Arg",
"transcript": "ENST00000397850.6",
"protein_id": "ENSP00000380948.2",
"transcript_support_level": 5,
"aa_start": 488,
"aa_end": null,
"aa_length": 769,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1917,
"cdna_end": null,
"cdna_length": 3178,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1464G>A",
"hgvs_p": "p.Arg488Arg",
"transcript": "ENST00000397857.5",
"protein_id": "ENSP00000380955.1",
"transcript_support_level": 5,
"aa_start": 488,
"aa_end": null,
"aa_length": 769,
"cds_start": 1464,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1552,
"cdna_end": null,
"cdna_length": 2813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1257G>A",
"hgvs_p": "p.Arg419Arg",
"transcript": "NM_001303238.2",
"protein_id": "NP_001290167.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 700,
"cds_start": 1257,
"cds_end": null,
"cds_length": 2103,
"cdna_start": 1589,
"cdna_end": null,
"cdna_length": 2850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1257G>A",
"hgvs_p": "p.Arg419Arg",
"transcript": "XM_006724001.3",
"protein_id": "XP_006724064.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 700,
"cds_start": 1257,
"cds_end": null,
"cds_length": 2103,
"cdna_start": 1591,
"cdna_end": null,
"cdna_length": 2852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "c.1257G>A",
"hgvs_p": "p.Arg419Arg",
"transcript": "XM_047440763.1",
"protein_id": "XP_047296719.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 700,
"cds_start": 1257,
"cds_end": null,
"cds_length": 2103,
"cdna_start": 1634,
"cdna_end": null,
"cdna_length": 2895,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "n.864G>A",
"hgvs_p": null,
"transcript": "ENST00000475170.5",
"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": 2125,
"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": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "n.*1291G>A",
"hgvs_p": null,
"transcript": "ENST00000523323.5",
"protein_id": "ENSP00000427732.1",
"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": 2823,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "n.671G>A",
"hgvs_p": null,
"transcript": "ENST00000696946.1",
"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": 1920,
"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": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"hgvs_c": "n.*1291G>A",
"hgvs_p": null,
"transcript": "ENST00000523323.5",
"protein_id": "ENSP00000427732.1",
"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": 2823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ITGB2",
"gene_hgnc_id": 6155,
"dbsnp": "rs202051683",
"frequency_reference_population": 0.00014504504,
"hom_count_reference_population": 0,
"allele_count_reference_population": 234,
"gnomad_exomes_af": 0.000152632,
"gnomad_genomes_af": 0.0000722429,
"gnomad_exomes_ac": 223,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.44999998807907104,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.459,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BS1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000652462.1",
"gene_symbol": "ITGB2",
"hgnc_id": 6155,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1464G>A",
"hgvs_p": "p.Arg488Arg"
}
],
"clinvar_disease": "ITGB2-related disorder,Leukocyte adhesion deficiency 1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Leukocyte adhesion deficiency 1|ITGB2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}