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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: 19-10333927-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=10333927&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 10333927,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000160262.10",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.1574G>A",
"hgvs_p": "p.Ser525Asn",
"transcript": "NM_002162.5",
"protein_id": "NP_002153.2",
"transcript_support_level": null,
"aa_start": 525,
"aa_end": null,
"aa_length": 547,
"cds_start": 1574,
"cds_end": null,
"cds_length": 1644,
"cdna_start": 1584,
"cdna_end": null,
"cdna_length": 1735,
"mane_select": "ENST00000160262.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.1574G>A",
"hgvs_p": "p.Ser525Asn",
"transcript": "ENST00000160262.10",
"protein_id": "ENSP00000160262.3",
"transcript_support_level": 1,
"aa_start": 525,
"aa_end": null,
"aa_length": 547,
"cds_start": 1574,
"cds_end": null,
"cds_length": 1644,
"cdna_start": 1584,
"cdna_end": null,
"cdna_length": 1735,
"mane_select": "NM_002162.5",
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "n.1876G>A",
"hgvs_p": null,
"transcript": "ENST00000589261.5",
"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": 2024,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.1343G>A",
"hgvs_p": "p.Ser448Asn",
"transcript": "NM_001320606.2",
"protein_id": "NP_001307535.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 470,
"cds_start": 1343,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 1881,
"cdna_end": null,
"cdna_length": 2032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.1286G>A",
"hgvs_p": "p.Ser429Asn",
"transcript": "NM_001320605.2",
"protein_id": "NP_001307534.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 451,
"cds_start": 1286,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1296,
"cdna_end": null,
"cdna_length": 1447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.989G>A",
"hgvs_p": "p.Ser330Asn",
"transcript": "NM_001395374.1",
"protein_id": "NP_001382303.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 352,
"cds_start": 989,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 1055,
"cdna_end": null,
"cdna_length": 1206,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.791G>A",
"hgvs_p": "p.Ser264Asn",
"transcript": "NM_001320608.2",
"protein_id": "NP_001307537.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 286,
"cds_start": 791,
"cds_end": null,
"cds_length": 861,
"cdna_start": 1901,
"cdna_end": null,
"cdna_length": 2052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.701G>A",
"hgvs_p": "p.Ser234Asn",
"transcript": "NM_001395375.1",
"protein_id": "NP_001382304.1",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 256,
"cds_start": 701,
"cds_end": null,
"cds_length": 771,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Ser189Asn",
"transcript": "NM_001395376.1",
"protein_id": "NP_001382305.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 211,
"cds_start": 566,
"cds_end": null,
"cds_length": 636,
"cdna_start": 675,
"cdna_end": null,
"cdna_length": 826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "c.566G>A",
"hgvs_p": "p.Ser189Asn",
"transcript": "ENST00000706691.1",
"protein_id": "ENSP00000516505.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 211,
"cds_start": 566,
"cds_end": null,
"cds_length": 636,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 946,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "n.2340G>A",
"hgvs_p": null,
"transcript": "ENST00000587992.1",
"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": 2491,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "n.1906G>A",
"hgvs_p": null,
"transcript": "ENST00000589900.5",
"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": 2057,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "n.509G>A",
"hgvs_p": null,
"transcript": "ENST00000592945.1",
"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": 658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000274425",
"gene_hgnc_id": null,
"hgvs_c": "n.492C>T",
"hgvs_p": null,
"transcript": "ENST00000612689.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 2813,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "n.761G>A",
"hgvs_p": null,
"transcript": "ENST00000706692.1",
"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": 911,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "n.*366G>A",
"hgvs_p": null,
"transcript": "ENST00000706693.1",
"protein_id": "ENSP00000516506.1",
"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": 855,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "n.*366G>A",
"hgvs_p": null,
"transcript": "ENST00000706693.1",
"protein_id": "ENSP00000516506.1",
"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": 855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"hgvs_c": "n.*48G>A",
"hgvs_p": null,
"transcript": "ENST00000592439.1",
"protein_id": null,
"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": 905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ICAM3",
"gene_hgnc_id": 5346,
"dbsnp": "rs2230399",
"frequency_reference_population": 6.840563e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84056e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.059627920389175415,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.02,
"revel_prediction": "Benign",
"alphamissense_score": 0.0891,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.221,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000160262.10",
"gene_symbol": "ICAM3",
"hgnc_id": 5346,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1574G>A",
"hgvs_p": "p.Ser525Asn"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000612689.1",
"gene_symbol": "ENSG00000274425",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.492C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}