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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: 6-107876571-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=107876571&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 107876571,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_007214.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.2027C>T",
"hgvs_p": "p.Thr676Ile",
"transcript": "NM_007214.5",
"protein_id": "NP_009145.1",
"transcript_support_level": null,
"aa_start": 676,
"aa_end": null,
"aa_length": 760,
"cds_start": 2027,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000369002.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007214.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.2027C>T",
"hgvs_p": "p.Thr676Ile",
"transcript": "ENST00000369002.9",
"protein_id": "ENSP00000357998.4",
"transcript_support_level": 1,
"aa_start": 676,
"aa_end": null,
"aa_length": 760,
"cds_start": 2027,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007214.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369002.9"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "n.830C>T",
"hgvs_p": null,
"transcript": "ENST00000459782.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000459782.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.2114C>T",
"hgvs_p": "p.Thr705Ile",
"transcript": "ENST00000884697.1",
"protein_id": "ENSP00000554756.1",
"transcript_support_level": null,
"aa_start": 705,
"aa_end": null,
"aa_length": 789,
"cds_start": 2114,
"cds_end": null,
"cds_length": 2370,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884697.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.2108C>T",
"hgvs_p": "p.Thr703Ile",
"transcript": "ENST00000884696.1",
"protein_id": "ENSP00000554755.1",
"transcript_support_level": null,
"aa_start": 703,
"aa_end": null,
"aa_length": 787,
"cds_start": 2108,
"cds_end": null,
"cds_length": 2364,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884696.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.2105C>T",
"hgvs_p": "p.Thr702Ile",
"transcript": "ENST00000955590.1",
"protein_id": "ENSP00000625649.1",
"transcript_support_level": null,
"aa_start": 702,
"aa_end": null,
"aa_length": 786,
"cds_start": 2105,
"cds_end": null,
"cds_length": 2361,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955590.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.2024C>T",
"hgvs_p": "p.Thr675Ile",
"transcript": "ENST00000884693.1",
"protein_id": "ENSP00000554752.1",
"transcript_support_level": null,
"aa_start": 675,
"aa_end": null,
"aa_length": 759,
"cds_start": 2024,
"cds_end": null,
"cds_length": 2280,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884693.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.1976C>T",
"hgvs_p": "p.Thr659Ile",
"transcript": "ENST00000938726.1",
"protein_id": "ENSP00000608785.1",
"transcript_support_level": null,
"aa_start": 659,
"aa_end": null,
"aa_length": 743,
"cds_start": 1976,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938726.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.1853C>T",
"hgvs_p": "p.Thr618Ile",
"transcript": "ENST00000938728.1",
"protein_id": "ENSP00000608787.1",
"transcript_support_level": null,
"aa_start": 618,
"aa_end": null,
"aa_length": 702,
"cds_start": 1853,
"cds_end": null,
"cds_length": 2109,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938728.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.1799C>T",
"hgvs_p": "p.Thr600Ile",
"transcript": "ENST00000955591.1",
"protein_id": "ENSP00000625650.1",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 684,
"cds_start": 1799,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955591.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.1766C>T",
"hgvs_p": "p.Thr589Ile",
"transcript": "ENST00000884695.1",
"protein_id": "ENSP00000554754.1",
"transcript_support_level": null,
"aa_start": 589,
"aa_end": null,
"aa_length": 673,
"cds_start": 1766,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884695.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.977C>T",
"hgvs_p": "p.Thr326Ile",
"transcript": "ENST00000938727.1",
"protein_id": "ENSP00000608786.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 410,
"cds_start": 977,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938727.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Thr620Ile",
"transcript": "XM_047418130.1",
"protein_id": "XP_047274086.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 704,
"cds_start": 1859,
"cds_end": null,
"cds_length": 2115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418130.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.1607C>T",
"hgvs_p": "p.Thr536Ile",
"transcript": "XM_047418131.1",
"protein_id": "XP_047274087.1",
"transcript_support_level": null,
"aa_start": 536,
"aa_end": null,
"aa_length": 620,
"cds_start": 1607,
"cds_end": null,
"cds_length": 1863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418131.1"
},
{
"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": 20,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "c.1936-3659C>T",
"hgvs_p": null,
"transcript": "ENST00000884694.1",
"protein_id": "ENSP00000554753.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 727,
"cds_start": null,
"cds_end": null,
"cds_length": 2184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884694.1"
},
{
"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": "SEC63",
"gene_hgnc_id": 21082,
"hgvs_c": "n.674C>T",
"hgvs_p": null,
"transcript": "ENST00000473746.1",
"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": "ENST00000473746.1"
}
],
"gene_symbol": "SEC63",
"gene_hgnc_id": 21082,
"dbsnp": "rs61733388",
"frequency_reference_population": 0.021574927,
"hom_count_reference_population": 454,
"allele_count_reference_population": 34042,
"gnomad_exomes_af": 0.0220302,
"gnomad_genomes_af": 0.0171538,
"gnomad_exomes_ac": 31515,
"gnomad_genomes_ac": 2527,
"gnomad_exomes_homalt": 427,
"gnomad_genomes_homalt": 27,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006633669137954712,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.128,
"revel_prediction": "Benign",
"alphamissense_score": 0.0958,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.198,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_007214.5",
"gene_symbol": "SEC63",
"hgnc_id": 21082,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2027C>T",
"hgvs_p": "p.Thr676Ile"
}
],
"clinvar_disease": "Polycystic liver disease 2,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"phenotype_combined": "Polycystic liver disease 2|not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}