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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: 4-98507685-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=98507685&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 98507685,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005723.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.125A>G",
"hgvs_p": "p.Asn42Ser",
"transcript": "NM_005723.4",
"protein_id": "NP_005714.2",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 268,
"cds_start": 125,
"cds_end": null,
"cds_length": 807,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 3347,
"mane_select": "ENST00000305798.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.125A>G",
"hgvs_p": "p.Asn42Ser",
"transcript": "ENST00000305798.8",
"protein_id": "ENSP00000307701.3",
"transcript_support_level": 1,
"aa_start": 42,
"aa_end": null,
"aa_length": 268,
"cds_start": 125,
"cds_end": null,
"cds_length": 807,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 3347,
"mane_select": "NM_005723.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.125A>G",
"hgvs_p": "p.Asn42Ser",
"transcript": "XM_005262680.2",
"protein_id": "XP_005262737.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 219,
"cds_start": 125,
"cds_end": null,
"cds_length": 660,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 3200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.125A>G",
"hgvs_p": "p.Asn42Ser",
"transcript": "XM_047449476.1",
"protein_id": "XP_047305432.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 193,
"cds_start": 125,
"cds_end": null,
"cds_length": 582,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 1056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.125A>G",
"hgvs_p": "p.Asn42Ser",
"transcript": "XM_047449477.1",
"protein_id": "XP_047305433.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 144,
"cds_start": 125,
"cds_end": null,
"cds_length": 435,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 915,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "n.193A>G",
"hgvs_p": null,
"transcript": "ENST00000507167.1",
"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": 540,
"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": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "n.125A>G",
"hgvs_p": null,
"transcript": "ENST00000508798.5",
"protein_id": "ENSP00000421808.1",
"transcript_support_level": 5,
"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": 3242,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "n.103A>G",
"hgvs_p": null,
"transcript": "ENST00000509168.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 539,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "n.-89A>G",
"hgvs_p": null,
"transcript": "ENST00000511800.5",
"protein_id": "ENSP00000422548.1",
"transcript_support_level": 3,
"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": 581,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "n.95A>G",
"hgvs_p": null,
"transcript": "ENST00000515440.5",
"protein_id": "ENSP00000422351.1",
"transcript_support_level": 3,
"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": 605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.-89A>G",
"hgvs_p": null,
"transcript": "ENST00000505184.5",
"protein_id": "ENSP00000423916.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 197,
"cds_start": -4,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1191,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.-89A>G",
"hgvs_p": null,
"transcript": "ENST00000515287.5",
"protein_id": "ENSP00000423504.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 109,
"cds_start": -4,
"cds_end": null,
"cds_length": 331,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.-89A>G",
"hgvs_p": null,
"transcript": "ENST00000511651.5",
"protein_id": "ENSP00000426248.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 59,
"cds_start": -4,
"cds_end": null,
"cds_length": 180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 710,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "n.-89A>G",
"hgvs_p": null,
"transcript": "ENST00000511800.5",
"protein_id": "ENSP00000422548.1",
"transcript_support_level": 3,
"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": 581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.-89A>G",
"hgvs_p": null,
"transcript": "XM_047449472.1",
"protein_id": "XP_047305428.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 197,
"cds_start": -4,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3440,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.-89A>G",
"hgvs_p": null,
"transcript": "XM_047449473.1",
"protein_id": "XP_047305429.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 197,
"cds_start": -4,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.-89A>G",
"hgvs_p": null,
"transcript": "XM_047449475.1",
"protein_id": "XP_047305431.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 197,
"cds_start": -4,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251523",
"gene_hgnc_id": null,
"hgvs_c": "n.356-2117T>C",
"hgvs_p": null,
"transcript": "ENST00000505408.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 489,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"dbsnp": "rs776364653",
"frequency_reference_population": 0.000024833955,
"hom_count_reference_population": 0,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.0000246835,
"gnomad_genomes_af": 0.0000262757,
"gnomad_exomes_ac": 36,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09673342108726501,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.054,
"revel_prediction": "Benign",
"alphamissense_score": 0.0615,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.624,
"phylop100way_prediction": "Uncertain_significance",
"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": 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_005723.4",
"gene_symbol": "TSPAN5",
"hgnc_id": 17753,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.125A>G",
"hgvs_p": "p.Asn42Ser"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000505408.1",
"gene_symbol": "ENSG00000251523",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.356-2117T>C",
"hgvs_p": null
}
],
"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
}