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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: 22-20993712-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=20993712&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 20993712,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000646124.2",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.1311G>A",
"hgvs_p": "p.Trp437*",
"transcript": "NM_006767.4",
"protein_id": "NP_006758.2",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 840,
"cds_start": 1311,
"cds_end": null,
"cds_length": 2523,
"cdna_start": 1386,
"cdna_end": null,
"cdna_length": 4282,
"mane_select": "ENST00000646124.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.1311G>A",
"hgvs_p": "p.Trp437*",
"transcript": "ENST00000646124.2",
"protein_id": "ENSP00000496779.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 840,
"cds_start": 1311,
"cds_end": null,
"cds_length": 2523,
"cdna_start": 1386,
"cdna_end": null,
"cdna_length": 4282,
"mane_select": "NM_006767.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.1311G>A",
"hgvs_p": "p.Trp437*",
"transcript": "ENST00000700578.1",
"protein_id": "ENSP00000515073.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 813,
"cds_start": 1311,
"cds_end": null,
"cds_length": 2442,
"cdna_start": 1393,
"cdna_end": null,
"cdna_length": 4187,
"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": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285314",
"gene_hgnc_id": null,
"hgvs_c": "n.1457G>A",
"hgvs_p": null,
"transcript": "ENST00000479606.5",
"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": 3442,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.360G>A",
"hgvs_p": null,
"transcript": "ENST00000492480.1",
"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": 695,
"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": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.656G>A",
"hgvs_p": null,
"transcript": "ENST00000495142.6",
"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": 4499,
"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": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.*997G>A",
"hgvs_p": null,
"transcript": "ENST00000642151.1",
"protein_id": "ENSP00000495284.1",
"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": 3665,
"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": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.1333G>A",
"hgvs_p": null,
"transcript": "ENST00000643578.1",
"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": 4213,
"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": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.172G>A",
"hgvs_p": null,
"transcript": "ENST00000643710.1",
"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": 2857,
"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": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.890G>A",
"hgvs_p": null,
"transcript": "ENST00000646506.1",
"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": 4058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.*997G>A",
"hgvs_p": null,
"transcript": "ENST00000642151.1",
"protein_id": "ENSP00000495284.1",
"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": 3665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"dbsnp": "rs770933647",
"frequency_reference_population": 0.0000012396274,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.84384e-7,
"gnomad_genomes_af": 0.00000656944,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5199999809265137,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.685,
"phylop100way_prediction": "Pathogenic",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000646124.2",
"gene_symbol": "LZTR1",
"hgnc_id": 6742,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1311G>A",
"hgvs_p": "p.Trp437*"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000479606.5",
"gene_symbol": "ENSG00000285314",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1457G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Cardiovascular phenotype,Hereditary cancer-predisposing syndrome,LZTR1-related schwannomatosis,Noonan syndrome 2,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4",
"phenotype_combined": "Noonan syndrome 2|not provided|Hereditary cancer-predisposing syndrome;Cardiovascular phenotype|LZTR1-related schwannomatosis",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}