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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: 18-59333237-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=59333237&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 59333237,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005570.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"hgvs_c": "c.1228A>T",
"hgvs_p": "p.Met410Leu",
"transcript": "NM_005570.4",
"protein_id": "NP_005561.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 510,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 1249,
"cdna_end": null,
"cdna_length": 4824,
"mane_select": "ENST00000251047.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005570.4"
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"hgvs_c": "c.1228A>T",
"hgvs_p": "p.Met410Leu",
"transcript": "ENST00000251047.6",
"protein_id": "ENSP00000251047.4",
"transcript_support_level": 1,
"aa_start": 410,
"aa_end": null,
"aa_length": 510,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 1249,
"cdna_end": null,
"cdna_length": 4824,
"mane_select": "NM_005570.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000251047.6"
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"hgvs_c": "c.1255A>T",
"hgvs_p": "p.Met419Leu",
"transcript": "ENST00000963587.1",
"protein_id": "ENSP00000633646.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 519,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 1275,
"cdna_end": null,
"cdna_length": 3740,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963587.1"
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"hgvs_c": "c.1228A>T",
"hgvs_p": "p.Met410Leu",
"transcript": "ENST00000904707.1",
"protein_id": "ENSP00000574766.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 515,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1548,
"cdna_start": 1238,
"cdna_end": null,
"cdna_length": 4824,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904707.1"
},
{
"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": "LMAN1",
"gene_hgnc_id": 6631,
"hgvs_c": "n.455A>T",
"hgvs_p": null,
"transcript": "ENST00000587918.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 678,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000587918.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267677",
"gene_hgnc_id": null,
"hgvs_c": "n.288T>A",
"hgvs_p": null,
"transcript": "ENST00000767581.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 354,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000767581.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267677",
"gene_hgnc_id": null,
"hgvs_c": "n.232+8647T>A",
"hgvs_p": null,
"transcript": "ENST00000767578.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 595,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000767578.1"
}
],
"gene_symbol": "LMAN1",
"gene_hgnc_id": 6631,
"dbsnp": "rs2298711",
"frequency_reference_population": 0.13182023,
"hom_count_reference_population": 14988,
"allele_count_reference_population": 212548,
"gnomad_exomes_af": 0.13449,
"gnomad_genomes_af": 0.106165,
"gnomad_exomes_ac": 196412,
"gnomad_genomes_ac": 16136,
"gnomad_exomes_homalt": 13924,
"gnomad_genomes_homalt": 1064,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.001447141170501709,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.102,
"revel_prediction": "Benign",
"alphamissense_score": 0.1061,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.712,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_005570.4",
"gene_symbol": "LMAN1",
"hgnc_id": 6631,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1228A>T",
"hgvs_p": "p.Met410Leu"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000767581.1",
"gene_symbol": "ENSG00000267677",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.288T>A",
"hgvs_p": null
}
],
"clinvar_disease": " combined deficiency of, type 1,Factor V and factor VIII,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|Factor V and factor VIII, combined deficiency of, type 1|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}