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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: 1-201091993-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=201091993&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 201091993,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000362061.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Arg174Trp",
"transcript": "NM_000069.3",
"protein_id": "NP_000060.2",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 1873,
"cds_start": 520,
"cds_end": null,
"cds_length": 5622,
"cdna_start": 607,
"cdna_end": null,
"cdna_length": 6028,
"mane_select": "ENST00000362061.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Arg174Trp",
"transcript": "ENST00000362061.4",
"protein_id": "ENSP00000355192.3",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 1873,
"cds_start": 520,
"cds_end": null,
"cds_length": 5622,
"cdna_start": 607,
"cdna_end": null,
"cdna_length": 6028,
"mane_select": "NM_000069.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Arg174Trp",
"transcript": "ENST00000367338.7",
"protein_id": "ENSP00000356307.3",
"transcript_support_level": 5,
"aa_start": 174,
"aa_end": null,
"aa_length": 1854,
"cds_start": 520,
"cds_end": null,
"cds_length": 5565,
"cdna_start": 632,
"cdna_end": null,
"cdna_length": 5996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Arg174Trp",
"transcript": "ENST00000681874.1",
"protein_id": "ENSP00000505162.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 1853,
"cds_start": 520,
"cds_end": null,
"cds_length": 5562,
"cdna_start": 607,
"cdna_end": null,
"cdna_length": 5968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Arg174Trp",
"transcript": "XM_005245478.4",
"protein_id": "XP_005245535.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 1854,
"cds_start": 520,
"cds_end": null,
"cds_length": 5565,
"cdna_start": 607,
"cdna_end": null,
"cdna_length": 5971,
"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": 4,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "n.520C>T",
"hgvs_p": null,
"transcript": "ENST00000679417.1",
"protein_id": "ENSP00000506706.1",
"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": 6307,
"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": 4,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "n.520C>T",
"hgvs_p": null,
"transcript": "ENST00000680059.1",
"protein_id": "ENSP00000504944.1",
"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": 6054,
"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": 4,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "n.520C>T",
"hgvs_p": null,
"transcript": "ENST00000681078.1",
"protein_id": "ENSP00000506645.1",
"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": 6159,
"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": 4,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "n.520C>T",
"hgvs_p": null,
"transcript": "ENST00000681190.1",
"protein_id": "ENSP00000506428.1",
"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": 6077,
"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": 4,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"hgvs_c": "n.520C>T",
"hgvs_p": null,
"transcript": "ENST00000713699.1",
"protein_id": "ENSP00000519003.1",
"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": 6045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CACNA1S",
"gene_hgnc_id": 1397,
"dbsnp": "rs772226819",
"frequency_reference_population": 0.000018587223,
"hom_count_reference_population": 0,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.0000184695,
"gnomad_genomes_af": 0.0000197179,
"gnomad_exomes_ac": 27,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9509825706481934,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.91,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9483,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.321,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.08,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BS1_Supporting",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000362061.4",
"gene_symbol": "CACNA1S",
"hgnc_id": 1397,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.520C>T",
"hgvs_p": "p.Arg174Trp"
}
],
"clinvar_disease": " 1, 5, susceptibility to, type 1,Congenital myopathy 18,Hypokalemic periodic paralysis,Malignant hyperthermia,Malignant hyperthermia of anesthesia,Thyrotoxic periodic paralysis,desflurane response - Toxicity,enflurane response - Toxicity,halothane response - Toxicity,isoflurane response - Toxicity,methoxyflurane response - Toxicity,not provided,not specified,sevoflurane response - Toxicity,succinylcholine response - Toxicity",
"clinvar_classification": "drug response",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:5 LP:8 US:1 O:7",
"phenotype_combined": "Hypokalemic periodic paralysis, type 1;Malignant hyperthermia, susceptibility to, 5|not provided|enflurane response - Toxicity|halothane response - Toxicity|isoflurane response - Toxicity|methoxyflurane response - Toxicity|sevoflurane response - Toxicity|desflurane response - Toxicity|not specified|succinylcholine response - Toxicity|Malignant hyperthermia, susceptibility to, 5|Malignant hyperthermia of anesthesia|Thyrotoxic periodic paralysis, susceptibility to, 1;Hypokalemic periodic paralysis, type 1;Malignant hyperthermia, susceptibility to, 5;Congenital myopathy 18",
"pathogenicity_classification_combined": "drug response",
"custom_annotations": null
}
],
"message": null
}