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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: 7-22160522-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=22160522&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 22160522,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000665637.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.1522C>T",
"hgvs_p": "p.Arg508Cys",
"transcript": "NM_012294.5",
"protein_id": "NP_036426.4",
"transcript_support_level": null,
"aa_start": 508,
"aa_end": null,
"aa_length": 883,
"cds_start": 1522,
"cds_end": null,
"cds_length": 2652,
"cdna_start": 1616,
"cdna_end": null,
"cdna_length": 6916,
"mane_select": "ENST00000665637.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.1522C>T",
"hgvs_p": "p.Arg508Cys",
"transcript": "ENST00000665637.1",
"protein_id": "ENSP00000499535.1",
"transcript_support_level": null,
"aa_start": 508,
"aa_end": null,
"aa_length": 883,
"cds_start": 1522,
"cds_end": null,
"cds_length": 2652,
"cdna_start": 1616,
"cdna_end": null,
"cdna_length": 6916,
"mane_select": "NM_012294.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.613C>T",
"hgvs_p": "p.Arg205Cys",
"transcript": "ENST00000401957.6",
"protein_id": "ENSP00000384044.1",
"transcript_support_level": 1,
"aa_start": 205,
"aa_end": null,
"aa_length": 580,
"cds_start": 613,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 6159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.1063C>T",
"hgvs_p": "p.Arg355Cys",
"transcript": "ENST00000344041.10",
"protein_id": "ENSP00000343656.6",
"transcript_support_level": 5,
"aa_start": 355,
"aa_end": null,
"aa_length": 730,
"cds_start": 1063,
"cds_end": null,
"cds_length": 2193,
"cdna_start": 1376,
"cdna_end": null,
"cdna_length": 6621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.613C>T",
"hgvs_p": "p.Arg205Cys",
"transcript": "NM_001367600.2",
"protein_id": "NP_001354529.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 580,
"cds_start": 613,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 5997,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.613C>T",
"hgvs_p": "p.Arg205Cys",
"transcript": "NM_001367601.1",
"protein_id": "NP_001354530.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 567,
"cds_start": 613,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 1827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.277C>T",
"hgvs_p": "p.Arg93Cys",
"transcript": "NM_001367602.2",
"protein_id": "NP_001354531.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 468,
"cds_start": 277,
"cds_end": null,
"cds_length": 1407,
"cdna_start": 881,
"cdna_end": null,
"cdna_length": 6181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.613C>T",
"hgvs_p": "p.Arg205Cys",
"transcript": "NM_001367603.1",
"protein_id": "NP_001354532.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 248,
"cds_start": 613,
"cds_end": null,
"cds_length": 747,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 1663,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.277C>T",
"hgvs_p": "p.Arg93Cys",
"transcript": "ENST00000458533.5",
"protein_id": "ENSP00000415664.1",
"transcript_support_level": 5,
"aa_start": 93,
"aa_end": null,
"aa_length": 141,
"cds_start": 277,
"cds_end": null,
"cds_length": 426,
"cdna_start": 720,
"cdna_end": null,
"cdna_length": 869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Arg383Cys",
"transcript": "XM_017012837.3",
"protein_id": "XP_016868326.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 758,
"cds_start": 1147,
"cds_end": null,
"cds_length": 2277,
"cdna_start": 1277,
"cdna_end": null,
"cdna_length": 6577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.535C>T",
"hgvs_p": "p.Arg179Cys",
"transcript": "XM_011515652.3",
"protein_id": "XP_011513954.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 554,
"cds_start": 535,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 15937,
"cdna_end": null,
"cdna_length": 21237,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.535C>T",
"hgvs_p": "p.Arg179Cys",
"transcript": "XM_047421083.1",
"protein_id": "XP_047277039.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 554,
"cds_start": 535,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 15811,
"cdna_end": null,
"cdna_length": 21111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "c.535C>T",
"hgvs_p": "p.Arg179Cys",
"transcript": "XM_047421084.1",
"protein_id": "XP_047277040.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 554,
"cds_start": 535,
"cds_end": null,
"cds_length": 1665,
"cdna_start": 15093,
"cdna_end": null,
"cdna_length": 20393,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "n.*352C>T",
"hgvs_p": null,
"transcript": "ENST00000451559.1",
"protein_id": "ENSP00000403956.1",
"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": 836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"hgvs_c": "n.*352C>T",
"hgvs_p": null,
"transcript": "ENST00000451559.1",
"protein_id": "ENSP00000403956.1",
"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": 836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RAPGEF5",
"gene_hgnc_id": 16862,
"dbsnp": "rs374326170",
"frequency_reference_population": 0.000029865048,
"hom_count_reference_population": 0,
"allele_count_reference_population": 46,
"gnomad_exomes_af": 0.0000280944,
"gnomad_genomes_af": 0.0000460272,
"gnomad_exomes_ac": 39,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.47838079929351807,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.292,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.549,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.246,
"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": 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": "ENST00000665637.1",
"gene_symbol": "RAPGEF5",
"hgnc_id": 16862,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1522C>T",
"hgvs_p": "p.Arg508Cys"
}
],
"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
}