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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: 2-219435093-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=219435093&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 219435093,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005876.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "NM_005876.5",
"protein_id": "NP_005867.3",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 3267,
"cds_start": 116,
"cds_end": null,
"cds_length": 9804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000312358.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005876.5"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "ENST00000312358.12",
"protein_id": "ENSP00000311684.7",
"transcript_support_level": 5,
"aa_start": 39,
"aa_end": null,
"aa_length": 3267,
"cds_start": 116,
"cds_end": null,
"cds_length": 9804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005876.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000312358.12"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "NM_001438924.1",
"protein_id": "NP_001425853.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 972,
"cds_start": 116,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438924.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "NM_001438925.1",
"protein_id": "NP_001425854.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 903,
"cds_start": 116,
"cds_end": null,
"cds_length": 2712,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438925.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_011510479.3",
"protein_id": "XP_011508781.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 3277,
"cds_start": 116,
"cds_end": null,
"cds_length": 9834,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510479.3"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_047442891.1",
"protein_id": "XP_047298847.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 3269,
"cds_start": 116,
"cds_end": null,
"cds_length": 9810,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442891.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_047442892.1",
"protein_id": "XP_047298848.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 3218,
"cds_start": 116,
"cds_end": null,
"cds_length": 9657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442892.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_047442893.1",
"protein_id": "XP_047298849.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 3216,
"cds_start": 116,
"cds_end": null,
"cds_length": 9651,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442893.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_047442894.1",
"protein_id": "XP_047298850.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 3208,
"cds_start": 116,
"cds_end": null,
"cds_length": 9627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442894.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_047442895.1",
"protein_id": "XP_047298851.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 3147,
"cds_start": 116,
"cds_end": null,
"cds_length": 9444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442895.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_017003159.3",
"protein_id": "XP_016858648.2",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 2632,
"cds_start": 116,
"cds_end": null,
"cds_length": 7899,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003159.3"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_047442901.1",
"protein_id": "XP_047298857.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 1728,
"cds_start": 116,
"cds_end": null,
"cds_length": 5187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442901.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_017003161.3",
"protein_id": "XP_016858650.2",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 982,
"cds_start": 116,
"cds_end": null,
"cds_length": 2949,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003161.3"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_047442902.1",
"protein_id": "XP_047298858.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 913,
"cds_start": 116,
"cds_end": null,
"cds_length": 2742,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442902.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_024452526.2",
"protein_id": "XP_024308294.2",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 911,
"cds_start": 116,
"cds_end": null,
"cds_length": 2736,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024452526.2"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala",
"transcript": "XM_047442906.1",
"protein_id": "XP_047298862.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 852,
"cds_start": 116,
"cds_end": null,
"cds_length": 2559,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442906.1"
}
],
"gene_symbol": "SPEG",
"gene_hgnc_id": 16901,
"dbsnp": "rs565137573",
"frequency_reference_population": 0.0015160409,
"hom_count_reference_population": 32,
"allele_count_reference_population": 2216,
"gnomad_exomes_af": 0.000676577,
"gnomad_genomes_af": 0.00874034,
"gnomad_exomes_ac": 886,
"gnomad_genomes_ac": 1330,
"gnomad_exomes_homalt": 12,
"gnomad_genomes_homalt": 20,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0027749240398406982,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.048,
"revel_prediction": "Benign",
"alphamissense_score": 0.0945,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.17,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005876.5",
"gene_symbol": "SPEG",
"hgnc_id": 16901,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.116T>C",
"hgvs_p": "p.Val39Ala"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}