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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: 22-20991686-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=20991686&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 20991686,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006767.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys",
"transcript": "NM_006767.4",
"protein_id": "NP_006758.2",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 840,
"cds_start": 850,
"cds_end": null,
"cds_length": 2523,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000646124.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006767.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys",
"transcript": "ENST00000646124.2",
"protein_id": "ENSP00000496779.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 840,
"cds_start": 850,
"cds_end": null,
"cds_length": 2523,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006767.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000646124.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys",
"transcript": "ENST00000888029.1",
"protein_id": "ENSP00000558088.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 839,
"cds_start": 850,
"cds_end": null,
"cds_length": 2520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888029.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys",
"transcript": "ENST00000888032.1",
"protein_id": "ENSP00000558091.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 839,
"cds_start": 850,
"cds_end": null,
"cds_length": 2520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888032.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys",
"transcript": "ENST00000888030.1",
"protein_id": "ENSP00000558089.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 825,
"cds_start": 850,
"cds_end": null,
"cds_length": 2478,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888030.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys",
"transcript": "ENST00000700578.1",
"protein_id": "ENSP00000515073.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 813,
"cds_start": 850,
"cds_end": null,
"cds_length": 2442,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000700578.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys",
"transcript": "ENST00000916176.1",
"protein_id": "ENSP00000586235.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 803,
"cds_start": 850,
"cds_end": null,
"cds_length": 2412,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916176.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys",
"transcript": "ENST00000888031.1",
"protein_id": "ENSP00000558090.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 740,
"cds_start": 850,
"cds_end": null,
"cds_length": 2223,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888031.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285314",
"gene_hgnc_id": null,
"hgvs_c": "n.996C>T",
"hgvs_p": null,
"transcript": "ENST00000479606.5",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000479606.5"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.195C>T",
"hgvs_p": null,
"transcript": "ENST00000495142.6",
"protein_id": null,
"transcript_support_level": 3,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000495142.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.*540C>T",
"hgvs_p": null,
"transcript": "ENST00000497716.5",
"protein_id": "ENSP00000494153.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000497716.5"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.*536C>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000642151.1"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.872C>T",
"hgvs_p": null,
"transcript": "ENST00000643578.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000643578.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.429C>T",
"hgvs_p": null,
"transcript": "ENST00000646506.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000646506.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.*540C>T",
"hgvs_p": null,
"transcript": "ENST00000497716.5",
"protein_id": "ENSP00000494153.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000497716.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.*536C>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000642151.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.-50C>T",
"hgvs_p": null,
"transcript": "ENST00000461510.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000461510.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.-95C>T",
"hgvs_p": null,
"transcript": "ENST00000492480.1",
"protein_id": null,
"transcript_support_level": 3,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000492480.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.*416C>T",
"hgvs_p": null,
"transcript": "ENST00000414985.5",
"protein_id": "ENSP00000397247.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000414985.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"hgvs_c": "n.*7C>T",
"hgvs_p": null,
"transcript": "ENST00000480895.1",
"protein_id": null,
"transcript_support_level": 4,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000480895.1"
}
],
"gene_symbol": "LZTR1",
"gene_hgnc_id": 6742,
"dbsnp": "rs797045165",
"frequency_reference_population": 0.000006859232,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000688931,
"gnomad_genomes_af": 0.00000657229,
"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": 0.9867238998413086,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.801,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9923,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.983,
"phylop100way_prediction": "Benign",
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP3,PS3_Moderate,PM2_Supporting,PS4_Supporting,PS2",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PP3",
"PS3_Moderate",
"PM2_Supporting",
"PS4_Supporting",
"PS2"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_006767.4",
"gene_symbol": "LZTR1",
"hgnc_id": 6742,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.850C>T",
"hgvs_p": "p.Arg284Cys"
},
{
"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.996C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Cardiovascular phenotype,Hereditary cancer-predisposing syndrome,LZTR1-related disorder,LZTR1-related schwannomatosis,Noonan syndrome 10,Noonan syndrome 2,RASopathy,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:8 LP:2",
"phenotype_combined": "Noonan syndrome 10|not provided|LZTR1-related schwannomatosis;Noonan syndrome 10|Hereditary cancer-predisposing syndrome;Cardiovascular phenotype|LZTR1-related disorder|LZTR1-related schwannomatosis;Noonan syndrome 10;Noonan syndrome 2|RASopathy",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}