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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: 14-39040878-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=39040878&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 39040878,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_006364.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "E",
"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": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "c.1996C>G",
"hgvs_p": "p.Gln666Glu",
"transcript": "NM_006364.4",
"protein_id": "NP_006355.2",
"transcript_support_level": null,
"aa_start": 666,
"aa_end": null,
"aa_length": 765,
"cds_start": 1996,
"cds_end": null,
"cds_length": 2298,
"cdna_start": 2221,
"cdna_end": null,
"cdna_length": 3843,
"mane_select": "ENST00000307712.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": true,
"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": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "c.1996C>G",
"hgvs_p": "p.Gln666Glu",
"transcript": "ENST00000307712.11",
"protein_id": "ENSP00000306881.6",
"transcript_support_level": 1,
"aa_start": 666,
"aa_end": null,
"aa_length": 765,
"cds_start": 1996,
"cds_end": null,
"cds_length": 2298,
"cdna_start": 2221,
"cdna_end": null,
"cdna_length": 3843,
"mane_select": "NM_006364.4",
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "n.556C>G",
"hgvs_p": null,
"transcript": "ENST00000554615.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 3813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"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": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "c.1909C>G",
"hgvs_p": "p.Gln637Glu",
"transcript": "ENST00000545328.6",
"protein_id": "ENSP00000445393.2",
"transcript_support_level": 2,
"aa_start": 637,
"aa_end": null,
"aa_length": 736,
"cds_start": 1909,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 2134,
"cdna_end": null,
"cdna_length": 2734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "c.1390C>G",
"hgvs_p": "p.Gln464Glu",
"transcript": "ENST00000537403.5",
"protein_id": "ENSP00000444193.1",
"transcript_support_level": 2,
"aa_start": 464,
"aa_end": null,
"aa_length": 563,
"cds_start": 1390,
"cds_end": null,
"cds_length": 1692,
"cdna_start": 2593,
"cdna_end": null,
"cdna_length": 4215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"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": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "c.2068C>G",
"hgvs_p": "p.Gln690Glu",
"transcript": "XM_005267262.2",
"protein_id": "XP_005267319.1",
"transcript_support_level": null,
"aa_start": 690,
"aa_end": null,
"aa_length": 789,
"cds_start": 2068,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 2293,
"cdna_end": null,
"cdna_length": 3915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"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": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "c.2068C>G",
"hgvs_p": "p.Gln690Glu",
"transcript": "XM_011536355.4",
"protein_id": "XP_011534657.1",
"transcript_support_level": null,
"aa_start": 690,
"aa_end": null,
"aa_length": 772,
"cds_start": 2068,
"cds_end": null,
"cds_length": 2319,
"cdna_start": 2293,
"cdna_end": null,
"cdna_length": 2667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"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": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "c.1996C>G",
"hgvs_p": "p.Gln666Glu",
"transcript": "XM_017020928.3",
"protein_id": "XP_016876417.1",
"transcript_support_level": null,
"aa_start": 666,
"aa_end": null,
"aa_length": 748,
"cds_start": 1996,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 2221,
"cdna_end": null,
"cdna_length": 2589,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC23A",
"gene_hgnc_id": 10701,
"hgvs_c": "n.367C>G",
"hgvs_p": null,
"transcript": "ENST00000555363.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SEC23A",
"gene_hgnc_id": 10701,
"dbsnp": "rs1318208043",
"frequency_reference_population": 0.000006572893,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657289,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6333836317062378,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.217,
"revel_prediction": "Benign",
"alphamissense_score": 0.1581,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.801,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006364.4",
"gene_symbol": "SEC23A",
"hgnc_id": 10701,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1996C>G",
"hgvs_p": "p.Gln666Glu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}