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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: 3-101332803-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=101332803&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 101332803,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000394095.7",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2540A>G",
"hgvs_p": "p.Asn847Ser",
"transcript": "NM_020654.5",
"protein_id": "NP_065705.3",
"transcript_support_level": null,
"aa_start": 847,
"aa_end": null,
"aa_length": 1050,
"cds_start": 2540,
"cds_end": null,
"cds_length": 3153,
"cdna_start": 2622,
"cdna_end": null,
"cdna_length": 4973,
"mane_select": "ENST00000394095.7",
"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": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2540A>G",
"hgvs_p": "p.Asn847Ser",
"transcript": "ENST00000394095.7",
"protein_id": "ENSP00000377655.2",
"transcript_support_level": 1,
"aa_start": 847,
"aa_end": null,
"aa_length": 1050,
"cds_start": 2540,
"cds_end": null,
"cds_length": 3153,
"cdna_start": 2622,
"cdna_end": null,
"cdna_length": 4973,
"mane_select": "NM_020654.5",
"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": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2441A>G",
"hgvs_p": "p.Asn814Ser",
"transcript": "ENST00000348610.3",
"protein_id": "ENSP00000342159.3",
"transcript_support_level": 1,
"aa_start": 814,
"aa_end": null,
"aa_length": 1017,
"cds_start": 2441,
"cds_end": null,
"cds_length": 3054,
"cdna_start": 2583,
"cdna_end": null,
"cdna_length": 3272,
"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": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2345A>G",
"hgvs_p": "p.Asn782Ser",
"transcript": "ENST00000394094.6",
"protein_id": "ENSP00000377654.2",
"transcript_support_level": 1,
"aa_start": 782,
"aa_end": null,
"aa_length": 985,
"cds_start": 2345,
"cds_end": null,
"cds_length": 2958,
"cdna_start": 2420,
"cdna_end": null,
"cdna_length": 4703,
"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": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2342A>G",
"hgvs_p": "p.Asn781Ser",
"transcript": "ENST00000314261.11",
"protein_id": "ENSP00000313624.7",
"transcript_support_level": 1,
"aa_start": 781,
"aa_end": null,
"aa_length": 984,
"cds_start": 2342,
"cds_end": null,
"cds_length": 2955,
"cdna_start": 2453,
"cdna_end": null,
"cdna_length": 4736,
"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": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2048A>G",
"hgvs_p": "p.Asn683Ser",
"transcript": "ENST00000394091.5",
"protein_id": "ENSP00000377651.1",
"transcript_support_level": 1,
"aa_start": 683,
"aa_end": null,
"aa_length": 886,
"cds_start": 2048,
"cds_end": null,
"cds_length": 2661,
"cdna_start": 2151,
"cdna_end": null,
"cdna_length": 4434,
"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": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.104A>G",
"hgvs_p": "p.Asn35Ser",
"transcript": "ENST00000394085.7",
"protein_id": "ENSP00000377647.3",
"transcript_support_level": 1,
"aa_start": 35,
"aa_end": null,
"aa_length": 238,
"cds_start": 104,
"cds_end": null,
"cds_length": 717,
"cdna_start": 467,
"cdna_end": null,
"cdna_length": 1483,
"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": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2441A>G",
"hgvs_p": "p.Asn814Ser",
"transcript": "NM_001282802.2",
"protein_id": "NP_001269731.1",
"transcript_support_level": null,
"aa_start": 814,
"aa_end": null,
"aa_length": 1017,
"cds_start": 2441,
"cds_end": null,
"cds_length": 3054,
"cdna_start": 2572,
"cdna_end": null,
"cdna_length": 4923,
"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": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2345A>G",
"hgvs_p": "p.Asn782Ser",
"transcript": "NM_001077203.3",
"protein_id": "NP_001070671.1",
"transcript_support_level": null,
"aa_start": 782,
"aa_end": null,
"aa_length": 985,
"cds_start": 2345,
"cds_end": null,
"cds_length": 2958,
"cdna_start": 2427,
"cdna_end": null,
"cdna_length": 4778,
"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": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2342A>G",
"hgvs_p": "p.Asn781Ser",
"transcript": "NM_001282801.2",
"protein_id": "NP_001269730.1",
"transcript_support_level": null,
"aa_start": 781,
"aa_end": null,
"aa_length": 984,
"cds_start": 2342,
"cds_end": null,
"cds_length": 2955,
"cdna_start": 2424,
"cdna_end": null,
"cdna_length": 4775,
"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": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2048A>G",
"hgvs_p": "p.Asn683Ser",
"transcript": "NM_001282803.2",
"protein_id": "NP_001269732.1",
"transcript_support_level": null,
"aa_start": 683,
"aa_end": null,
"aa_length": 886,
"cds_start": 2048,
"cds_end": null,
"cds_length": 2661,
"cdna_start": 2179,
"cdna_end": null,
"cdna_length": 4530,
"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": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2543A>G",
"hgvs_p": "p.Asn848Ser",
"transcript": "XM_011513038.4",
"protein_id": "XP_011511340.1",
"transcript_support_level": null,
"aa_start": 848,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2543,
"cds_end": null,
"cds_length": 3156,
"cdna_start": 2625,
"cdna_end": null,
"cdna_length": 4976,
"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": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2348A>G",
"hgvs_p": "p.Asn783Ser",
"transcript": "XM_011513040.4",
"protein_id": "XP_011511342.1",
"transcript_support_level": null,
"aa_start": 783,
"aa_end": null,
"aa_length": 986,
"cds_start": 2348,
"cds_end": null,
"cds_length": 2961,
"cdna_start": 2430,
"cdna_end": null,
"cdna_length": 4781,
"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": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2345A>G",
"hgvs_p": "p.Asn782Ser",
"transcript": "XM_011513041.4",
"protein_id": "XP_011511343.1",
"transcript_support_level": null,
"aa_start": 782,
"aa_end": null,
"aa_length": 985,
"cds_start": 2345,
"cds_end": null,
"cds_length": 2958,
"cdna_start": 2427,
"cdna_end": null,
"cdna_length": 4778,
"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": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2246A>G",
"hgvs_p": "p.Asn749Ser",
"transcript": "XM_017006926.2",
"protein_id": "XP_016862415.1",
"transcript_support_level": null,
"aa_start": 749,
"aa_end": null,
"aa_length": 952,
"cds_start": 2246,
"cds_end": null,
"cds_length": 2859,
"cdna_start": 2377,
"cdna_end": null,
"cdna_length": 4728,
"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": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2150A>G",
"hgvs_p": "p.Asn717Ser",
"transcript": "XM_011513042.4",
"protein_id": "XP_011511344.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 920,
"cds_start": 2150,
"cds_end": null,
"cds_length": 2763,
"cdna_start": 2232,
"cdna_end": null,
"cdna_length": 4583,
"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": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2147A>G",
"hgvs_p": "p.Asn716Ser",
"transcript": "XM_005247662.6",
"protein_id": "XP_005247719.1",
"transcript_support_level": null,
"aa_start": 716,
"aa_end": null,
"aa_length": 919,
"cds_start": 2147,
"cds_end": null,
"cds_length": 2760,
"cdna_start": 2229,
"cdna_end": null,
"cdna_length": 4580,
"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": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.2051A>G",
"hgvs_p": "p.Asn684Ser",
"transcript": "XM_047448627.1",
"protein_id": "XP_047304583.1",
"transcript_support_level": null,
"aa_start": 684,
"aa_end": null,
"aa_length": 887,
"cds_start": 2051,
"cds_end": null,
"cds_length": 2664,
"cdna_start": 2182,
"cdna_end": null,
"cdna_length": 4533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"hgvs_c": "c.*87A>G",
"hgvs_p": null,
"transcript": "XM_047448628.1",
"protein_id": "XP_047304584.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 834,
"cds_start": -4,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SENP7",
"gene_hgnc_id": 30402,
"dbsnp": "rs202141841",
"frequency_reference_population": 0.000011518467,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.00000638094,
"gnomad_genomes_af": 0.0000591102,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05686202645301819,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.12,
"revel_prediction": "Benign",
"alphamissense_score": 0.0758,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.249,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000394095.7",
"gene_symbol": "SENP7",
"hgnc_id": 30402,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2540A>G",
"hgvs_p": "p.Asn847Ser"
}
],
"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
}