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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: 2-74552556-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=74552556&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 74552556,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000264094.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "NM_032603.5",
"protein_id": "NP_115992.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 753,
"cds_start": 79,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 158,
"cdna_end": null,
"cdna_length": 3689,
"mane_select": "ENST00000264094.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "ENST00000264094.8",
"protein_id": "ENSP00000264094.3",
"transcript_support_level": 1,
"aa_start": 27,
"aa_end": null,
"aa_length": 753,
"cds_start": 79,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 158,
"cdna_end": null,
"cdna_length": 3689,
"mane_select": "NM_032603.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DOK1",
"gene_hgnc_id": 2990,
"hgvs_c": "c.-357-2598G>C",
"hgvs_p": null,
"transcript": "ENST00000409429.5",
"protein_id": "ENSP00000387016.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 342,
"cds_start": -4,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "ENST00000409549.5",
"protein_id": "ENSP00000386696.1",
"transcript_support_level": 2,
"aa_start": 27,
"aa_end": null,
"aa_length": 697,
"cds_start": 79,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 2897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "NM_001289164.3",
"protein_id": "NP_001276093.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 608,
"cds_start": 79,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 158,
"cdna_end": null,
"cdna_length": 3254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "ENST00000393937.6",
"protein_id": "ENSP00000377512.2",
"transcript_support_level": 5,
"aa_start": 27,
"aa_end": null,
"aa_length": 608,
"cds_start": 79,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 174,
"cdna_end": null,
"cdna_length": 2398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "ENST00000409986.5",
"protein_id": "ENSP00000386545.1",
"transcript_support_level": 2,
"aa_start": 27,
"aa_end": null,
"aa_length": 586,
"cds_start": 79,
"cds_end": null,
"cds_length": 1761,
"cdna_start": 177,
"cdna_end": null,
"cdna_length": 2005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "ENST00000409249.5",
"protein_id": "ENSP00000387103.1",
"transcript_support_level": 5,
"aa_start": 27,
"aa_end": null,
"aa_length": 471,
"cds_start": 79,
"cds_end": null,
"cds_length": 1416,
"cdna_start": 92,
"cdna_end": null,
"cdna_length": 2431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "ENST00000413469.1",
"protein_id": "ENSP00000398260.1",
"transcript_support_level": 3,
"aa_start": 27,
"aa_end": null,
"aa_length": 302,
"cds_start": 79,
"cds_end": null,
"cds_length": 910,
"cdna_start": 170,
"cdna_end": null,
"cdna_length": 1001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "XM_011533134.3",
"protein_id": "XP_011531436.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 753,
"cds_start": 79,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 133,
"cdna_end": null,
"cdna_length": 3664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "XM_024453176.2",
"protein_id": "XP_024308944.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 753,
"cds_start": 79,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 196,
"cdna_end": null,
"cdna_length": 3727,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "XM_024453177.2",
"protein_id": "XP_024308945.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 753,
"cds_start": 79,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 350,
"cdna_end": null,
"cdna_length": 3881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala",
"transcript": "XM_024453178.2",
"protein_id": "XP_024308946.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 753,
"cds_start": 79,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 1425,
"cdna_end": null,
"cdna_length": 4956,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"hgvs_c": "n.92C>G",
"hgvs_p": null,
"transcript": "ENST00000484369.1",
"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": 762,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DOK1",
"gene_hgnc_id": 2990,
"hgvs_c": "c.-357-2598G>C",
"hgvs_p": null,
"transcript": "NM_001197260.2",
"protein_id": "NP_001184189.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 342,
"cds_start": -4,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "DOK1",
"gene_hgnc_id": 2990,
"hgvs_c": "n.262-2238G>C",
"hgvs_p": null,
"transcript": "ENST00000485132.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LOXL3",
"gene_hgnc_id": 13869,
"dbsnp": "rs146972503",
"frequency_reference_population": 0.0026918978,
"hom_count_reference_population": 14,
"allele_count_reference_population": 4339,
"gnomad_exomes_af": 0.00273515,
"gnomad_genomes_af": 0.00227756,
"gnomad_exomes_ac": 3992,
"gnomad_genomes_ac": 347,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005101799964904785,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.067,
"revel_prediction": "Benign",
"alphamissense_score": 0.057,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.36,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000264094.8",
"gene_symbol": "LOXL3",
"hgnc_id": 13869,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.79C>G",
"hgvs_p": "p.Pro27Ala"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001197260.2",
"gene_symbol": "DOK1",
"hgnc_id": 2990,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-357-2598G>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}