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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: 3-50159664-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=50159664&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 50159664,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_004186.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "NM_004186.5",
"protein_id": "NP_004177.3",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 785,
"cds_start": 42,
"cds_end": null,
"cds_length": 2358,
"cdna_start": 331,
"cdna_end": null,
"cdna_length": 3607,
"mane_select": "ENST00000002829.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "ENST00000002829.8",
"protein_id": "ENSP00000002829.3",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 785,
"cds_start": 42,
"cds_end": null,
"cds_length": 2358,
"cdna_start": 331,
"cdna_end": null,
"cdna_length": 3607,
"mane_select": "NM_004186.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "ENST00000434342.5",
"protein_id": "ENSP00000409859.1",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 754,
"cds_start": 42,
"cds_end": null,
"cds_length": 2265,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 3541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.-135-28C>T",
"hgvs_p": null,
"transcript": "ENST00000413852.5",
"protein_id": "ENSP00000388931.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 686,
"cds_start": -4,
"cds_end": null,
"cds_length": 2061,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "NM_001318800.2",
"protein_id": "NP_001305729.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 754,
"cds_start": 42,
"cds_end": null,
"cds_length": 2265,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 3543,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "ENST00000450338.5",
"protein_id": "ENSP00000398399.1",
"transcript_support_level": 5,
"aa_start": 14,
"aa_end": null,
"aa_length": 378,
"cds_start": 42,
"cds_end": null,
"cds_length": 1139,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 1693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "ENST00000414301.5",
"protein_id": "ENSP00000392588.1",
"transcript_support_level": 5,
"aa_start": 14,
"aa_end": null,
"aa_length": 263,
"cds_start": 42,
"cds_end": null,
"cds_length": 793,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "ENST00000426511.5",
"protein_id": "ENSP00000400549.1",
"transcript_support_level": 5,
"aa_start": 14,
"aa_end": null,
"aa_length": 91,
"cds_start": 42,
"cds_end": null,
"cds_length": 276,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "XM_005265381.5",
"protein_id": "XP_005265438.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 785,
"cds_start": 42,
"cds_end": null,
"cds_length": 2358,
"cdna_start": 876,
"cdna_end": null,
"cdna_length": 4152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "XM_011533998.3",
"protein_id": "XP_011532300.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 785,
"cds_start": 42,
"cds_end": null,
"cds_length": 2358,
"cdna_start": 180,
"cdna_end": null,
"cdna_length": 3456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "XM_047448699.1",
"protein_id": "XP_047304655.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 785,
"cds_start": 42,
"cds_end": null,
"cds_length": 2358,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 3636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "XM_005265382.5",
"protein_id": "XP_005265439.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 754,
"cds_start": 42,
"cds_end": null,
"cds_length": 2265,
"cdna_start": 331,
"cdna_end": null,
"cdna_length": 3514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "XM_047448700.1",
"protein_id": "XP_047304656.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 754,
"cds_start": 42,
"cds_end": null,
"cds_length": 2265,
"cdna_start": 180,
"cdna_end": null,
"cdna_length": 3363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "XM_047448701.1",
"protein_id": "XP_047304657.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 516,
"cds_start": 42,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 331,
"cdna_end": null,
"cdna_length": 1964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "XM_011534000.3",
"protein_id": "XP_011532302.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 512,
"cds_start": 42,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 331,
"cdna_end": null,
"cdna_length": 1922,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr",
"transcript": "XM_006713290.4",
"protein_id": "XP_006713353.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 484,
"cds_start": 42,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 331,
"cdna_end": null,
"cdna_length": 1759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"hgvs_c": "c.-135-28C>T",
"hgvs_p": null,
"transcript": "NM_001318798.2",
"protein_id": "NP_001305727.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 686,
"cds_start": -4,
"cds_end": null,
"cds_length": 2061,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SEMA3F",
"gene_hgnc_id": 10728,
"dbsnp": "rs1046953",
"frequency_reference_population": 0.41708347,
"hom_count_reference_population": 145180,
"allele_count_reference_population": 671793,
"gnomad_exomes_af": 0.42025,
"gnomad_genomes_af": 0.386714,
"gnomad_exomes_ac": 612973,
"gnomad_genomes_ac": 58820,
"gnomad_exomes_homalt": 133351,
"gnomad_genomes_homalt": 11829,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.943,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_004186.5",
"gene_symbol": "SEMA3F",
"hgnc_id": 10728,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.42C>T",
"hgvs_p": "p.Thr14Thr"
}
],
"clinvar_disease": "SEMA3F-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "SEMA3F-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}