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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: 16-25111950-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=25111950&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 25111950,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_016309.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.67G>T",
"hgvs_p": "p.Asp23Tyr",
"transcript": "NM_016309.3",
"protein_id": "NP_057393.2",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 334,
"cds_start": 67,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 1352,
"mane_select": "ENST00000399069.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.67G>T",
"hgvs_p": "p.Asp23Tyr",
"transcript": "ENST00000399069.8",
"protein_id": "ENSP00000382021.3",
"transcript_support_level": 1,
"aa_start": 23,
"aa_end": null,
"aa_length": 334,
"cds_start": 67,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 1352,
"mane_select": "NM_016309.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "n.67G>T",
"hgvs_p": null,
"transcript": "ENST00000380962.9",
"protein_id": "ENSP00000370349.5",
"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": 1529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.67G>T",
"hgvs_p": "p.Asp23Tyr",
"transcript": "NM_001032391.2",
"protein_id": "NP_001027563.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 279,
"cds_start": 67,
"cds_end": null,
"cds_length": 840,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 1187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.67G>T",
"hgvs_p": "p.Asp23Tyr",
"transcript": "ENST00000380966.8",
"protein_id": "ENSP00000370353.4",
"transcript_support_level": 2,
"aa_start": 23,
"aa_end": null,
"aa_length": 279,
"cds_start": 67,
"cds_end": null,
"cds_length": 840,
"cdna_start": 216,
"cdna_end": null,
"cdna_length": 989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.19G>T",
"hgvs_p": "p.Asp7Tyr",
"transcript": "ENST00000570981.1",
"protein_id": "ENSP00000459851.1",
"transcript_support_level": 2,
"aa_start": 7,
"aa_end": null,
"aa_length": 119,
"cds_start": 19,
"cds_end": null,
"cds_length": 360,
"cdna_start": 19,
"cdna_end": null,
"cdna_length": 612,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "n.67G>T",
"hgvs_p": null,
"transcript": "ENST00000564011.5",
"protein_id": "ENSP00000457741.1",
"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": 1168,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.-28G>T",
"hgvs_p": null,
"transcript": "XM_011545864.2",
"protein_id": "XP_011544166.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 357,
"cds_start": -4,
"cds_end": null,
"cds_length": 1074,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.-28G>T",
"hgvs_p": null,
"transcript": "XM_011545862.3",
"protein_id": "XP_011544164.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 302,
"cds_start": -4,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1350,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "n.24+182G>T",
"hgvs_p": null,
"transcript": "ENST00000577157.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 522,
"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": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.-120+182G>T",
"hgvs_p": null,
"transcript": "XM_047434197.1",
"protein_id": "XP_047290153.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 311,
"cds_start": -4,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1287,
"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": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"hgvs_c": "c.-188+182G>T",
"hgvs_p": null,
"transcript": "XM_005255354.5",
"protein_id": "XP_005255411.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 234,
"cds_start": -4,
"cds_end": null,
"cds_length": 705,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LCMT1",
"gene_hgnc_id": 17557,
"dbsnp": "rs370007375",
"frequency_reference_population": 0.0000068173763,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000684328,
"gnomad_genomes_af": 0.00000656875,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5964847803115845,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.344,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7006,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.004,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016309.3",
"gene_symbol": "LCMT1",
"hgnc_id": 17557,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.67G>T",
"hgvs_p": "p.Asp23Tyr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}