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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: 4-56811703-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56811703&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 56811703,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001271718.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.341C>G",
"hgvs_p": "p.Thr114Ser",
"transcript": "NM_001271718.2",
"protein_id": "NP_001258647.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 134,
"cds_start": 341,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000506738.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271718.2"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.341C>G",
"hgvs_p": "p.Thr114Ser",
"transcript": "ENST00000506738.6",
"protein_id": "ENSP00000425961.1",
"transcript_support_level": 2,
"aa_start": 114,
"aa_end": null,
"aa_length": 134,
"cds_start": 341,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001271718.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506738.6"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.191C>G",
"hgvs_p": "p.Thr64Ser",
"transcript": "ENST00000248701.8",
"protein_id": "ENSP00000248701.4",
"transcript_support_level": 1,
"aa_start": 64,
"aa_end": null,
"aa_length": 84,
"cds_start": 191,
"cds_end": null,
"cds_length": 255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000248701.8"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.296C>G",
"hgvs_p": "p.Thr99Ser",
"transcript": "NM_001271720.2",
"protein_id": "NP_001258649.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 119,
"cds_start": 296,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271720.2"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.296C>G",
"hgvs_p": "p.Thr99Ser",
"transcript": "ENST00000504762.1",
"protein_id": "ENSP00000423858.1",
"transcript_support_level": 2,
"aa_start": 99,
"aa_end": null,
"aa_length": 119,
"cds_start": 296,
"cds_end": null,
"cds_length": 360,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000504762.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.301C>G",
"hgvs_p": "p.Leu101Val",
"transcript": "NM_001271719.2",
"protein_id": "NP_001258648.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 103,
"cds_start": 301,
"cds_end": null,
"cds_length": 312,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271719.2"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.256C>G",
"hgvs_p": "p.Leu86Val",
"transcript": "NM_001271721.2",
"protein_id": "NP_001258650.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 88,
"cds_start": 256,
"cds_end": null,
"cds_length": 267,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271721.2"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.191C>G",
"hgvs_p": "p.Thr64Ser",
"transcript": "NM_021114.4",
"protein_id": "NP_066937.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 84,
"cds_start": 191,
"cds_end": null,
"cds_length": 255,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021114.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.206-1519C>G",
"hgvs_p": null,
"transcript": "NM_001271722.2",
"protein_id": "NP_001258651.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 134,
"cds_start": null,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271722.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.206-1519C>G",
"hgvs_p": null,
"transcript": "ENST00000618802.3",
"protein_id": "ENSP00000477722.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 134,
"cds_start": null,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000618802.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "c.250-1519C>G",
"hgvs_p": null,
"transcript": "ENST00000707144.1",
"protein_id": "ENSP00000516764.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 87,
"cds_start": null,
"cds_end": null,
"cds_length": 264,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000707144.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "n.94C>G",
"hgvs_p": null,
"transcript": "ENST00000509707.1",
"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": "ENST00000509707.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "n.478C>G",
"hgvs_p": null,
"transcript": "NR_073417.2",
"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": "pseudogene",
"feature": "NR_073417.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "n.518C>G",
"hgvs_p": null,
"transcript": "NR_073419.2",
"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": "pseudogene",
"feature": "NR_073419.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"hgvs_c": "n.307-1519C>G",
"hgvs_p": null,
"transcript": "NR_073418.1",
"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": "pseudogene",
"feature": "NR_073418.1"
}
],
"gene_symbol": "SPINK2",
"gene_hgnc_id": 11245,
"dbsnp": "rs368929102",
"frequency_reference_population": 0.000013155298,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131553,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09892141819000244,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.152,
"revel_prediction": "Benign",
"alphamissense_score": 0.1514,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.067,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.13,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001271718.2",
"gene_symbol": "SPINK2",
"hgnc_id": 11245,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.341C>G",
"hgvs_p": "p.Thr114Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}