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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: 1-201078005-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=201078005&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP3_Moderate",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CACNA1S",
"hgnc_id": 1397,
"hgvs_c": "c.1493G>A",
"hgvs_p": "p.Arg498His",
"inheritance_mode": "SD,AD,AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_000069.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS1",
"acmg_score": -2,
"allele_count_reference_population": 451,
"alphamissense_prediction": null,
"alphamissense_score": 0.4998,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.45,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 1, 5, susceptibility to, type 1,Congenital myopathy 18,Hypokalemic periodic paralysis,Inborn genetic diseases,Malignant hyperthermia,Thyrotoxic periodic paralysis,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:7 LB:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9183061122894287,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1873,
"aa_ref": "R",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6028,
"cdna_start": 1580,
"cds_end": null,
"cds_length": 5622,
"cds_start": 1493,
"consequences": [
"missense_variant"
],
"exon_count": 44,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_000069.3",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "c.1493G>A",
"hgvs_p": "p.Arg498His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000362061.4",
"protein_coding": true,
"protein_id": "NP_000060.2",
"strand": false,
"transcript": "NM_000069.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1873,
"aa_ref": "R",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6028,
"cdna_start": 1580,
"cds_end": null,
"cds_length": 5622,
"cds_start": 1493,
"consequences": [
"missense_variant"
],
"exon_count": 44,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000362061.4",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "c.1493G>A",
"hgvs_p": "p.Arg498His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000069.3",
"protein_coding": true,
"protein_id": "ENSP00000355192.3",
"strand": false,
"transcript": "ENST00000362061.4",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1854,
"aa_ref": "R",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5996,
"cdna_start": 1605,
"cds_end": null,
"cds_length": 5565,
"cds_start": 1493,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000367338.7",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "c.1493G>A",
"hgvs_p": "p.Arg498His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000356307.3",
"strand": false,
"transcript": "ENST00000367338.7",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1853,
"aa_ref": "R",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5968,
"cdna_start": 1580,
"cds_end": null,
"cds_length": 5562,
"cds_start": 1493,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000681874.1",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "c.1493G>A",
"hgvs_p": "p.Arg498His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000505162.1",
"strand": false,
"transcript": "ENST00000681874.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1854,
"aa_ref": "R",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5971,
"cdna_start": 1580,
"cds_end": null,
"cds_length": 5565,
"cds_start": 1493,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_005245478.4",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "c.1493G>A",
"hgvs_p": "p.Arg498His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005245535.1",
"strand": false,
"transcript": "XM_005245478.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6307,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 44,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000679417.1",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "n.*656G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506706.1",
"strand": false,
"transcript": "ENST00000679417.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6054,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 44,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000680059.1",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "n.1493G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000504944.1",
"strand": false,
"transcript": "ENST00000680059.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6159,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 44,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000681078.1",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "n.1493G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506645.1",
"strand": false,
"transcript": "ENST00000681078.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6077,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 45,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000681190.1",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "n.1493G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506428.1",
"strand": false,
"transcript": "ENST00000681190.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6045,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 44,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000713699.1",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "n.1493G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000519003.1",
"strand": false,
"transcript": "ENST00000713699.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6307,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 44,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000679417.1",
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"hgvs_c": "n.*656G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506706.1",
"strand": false,
"transcript": "ENST00000679417.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs150590855",
"effect": "missense_variant",
"frequency_reference_population": 0.0002794009,
"gene_hgnc_id": 1397,
"gene_symbol": "CACNA1S",
"gnomad_exomes_ac": 425,
"gnomad_exomes_af": 0.00029073,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 26,
"gnomad_genomes_af": 0.00017068,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not provided|Hypokalemic periodic paralysis, type 1;Malignant hyperthermia, susceptibility to, 5|Hypokalemic periodic paralysis, type 1|Hypokalemic periodic paralysis, type 1;Thyrotoxic periodic paralysis, susceptibility to, 1;Congenital myopathy 18;Malignant hyperthermia, susceptibility to, 5|Inborn genetic diseases|Malignant hyperthermia, susceptibility to, 5",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.876,
"pos": 201078005,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.928,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_000069.3"
}
]
}