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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: 11-62617186-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=62617186&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 62617186,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000265471.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Pro140Leu",
"transcript": "NM_012200.4",
"protein_id": "NP_036332.2",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 335,
"cds_start": 419,
"cds_end": null,
"cds_length": 1008,
"cdna_start": 458,
"cdna_end": null,
"cdna_length": 1452,
"mane_select": "ENST00000265471.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Pro140Leu",
"transcript": "ENST00000265471.10",
"protein_id": "ENSP00000265471.5",
"transcript_support_level": 1,
"aa_start": 140,
"aa_end": null,
"aa_length": 335,
"cds_start": 419,
"cds_end": null,
"cds_length": 1008,
"cdna_start": 458,
"cdna_end": null,
"cdna_length": 1452,
"mane_select": "NM_012200.4",
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "n.*541C>T",
"hgvs_p": null,
"transcript": "ENST00000532585.5",
"protein_id": "ENSP00000432604.1",
"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": 1534,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "n.*541C>T",
"hgvs_p": null,
"transcript": "ENST00000532585.5",
"protein_id": "ENSP00000432604.1",
"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": 1534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.398C>T",
"hgvs_p": "p.Pro133Leu",
"transcript": "NM_001288721.2",
"protein_id": "NP_001275650.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 328,
"cds_start": 398,
"cds_end": null,
"cds_length": 987,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 1691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Pro140Leu",
"transcript": "NM_001288722.2",
"protein_id": "NP_001275651.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 319,
"cds_start": 419,
"cds_end": null,
"cds_length": 960,
"cdna_start": 458,
"cdna_end": null,
"cdna_length": 1889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Pro140Leu",
"transcript": "ENST00000531383.5",
"protein_id": "ENSP00000431359.1",
"transcript_support_level": 2,
"aa_start": 140,
"aa_end": null,
"aa_length": 319,
"cds_start": 419,
"cds_end": null,
"cds_length": 960,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 2056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Pro140Leu",
"transcript": "NM_001288723.2",
"protein_id": "NP_001275652.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 315,
"cds_start": 419,
"cds_end": null,
"cds_length": 948,
"cdna_start": 458,
"cdna_end": null,
"cdna_length": 1893,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Pro140Leu",
"transcript": "ENST00000534026.5",
"protein_id": "ENSP00000432474.1",
"transcript_support_level": 2,
"aa_start": 140,
"aa_end": null,
"aa_length": 315,
"cds_start": 419,
"cds_end": null,
"cds_length": 948,
"cdna_start": 456,
"cdna_end": null,
"cdna_length": 1120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.488C>T",
"hgvs_p": "p.Pro163Leu",
"transcript": "ENST00000534715.1",
"protein_id": "ENSP00000432854.1",
"transcript_support_level": 5,
"aa_start": 163,
"aa_end": null,
"aa_length": 222,
"cds_start": 488,
"cds_end": null,
"cds_length": 669,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "c.398C>T",
"hgvs_p": "p.Pro133Leu",
"transcript": "XM_047426751.1",
"protein_id": "XP_047282707.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 328,
"cds_start": 398,
"cds_end": null,
"cds_length": 987,
"cdna_start": 1102,
"cdna_end": null,
"cdna_length": 2096,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "n.269C>T",
"hgvs_p": null,
"transcript": "ENST00000533303.1",
"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": 576,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"hgvs_c": "n.448C>T",
"hgvs_p": null,
"transcript": "NR_109991.2",
"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": 1442,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "B3GAT3",
"gene_hgnc_id": 923,
"dbsnp": "rs879255269",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8975107669830322,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.53,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3872,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.633,
"phylop100way_prediction": "Uncertain_significance",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000265471.10",
"gene_symbol": "B3GAT3",
"hgnc_id": 923,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Pro140Leu"
}
],
"clinvar_disease": " AND CRANIOFACIAL DYSMORPHISM WITHOUT CONGENITAL HEART DEFECTS, SHORT STATURE,MULTIPLE JOINT DISLOCATIONS",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "MULTIPLE JOINT DISLOCATIONS, SHORT STATURE, AND CRANIOFACIAL DYSMORPHISM WITHOUT CONGENITAL HEART DEFECTS",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}