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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: 8-7860667-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=7860667&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 7860667,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000642566.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.236G>A",
"hgvs_p": "p.Arg79Lys",
"transcript": "NM_001395484.1",
"protein_id": "NP_001382413.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 133,
"cds_start": 236,
"cds_end": null,
"cds_length": 402,
"cdna_start": 275,
"cdna_end": null,
"cdna_length": 551,
"mane_select": "ENST00000642566.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.236G>A",
"hgvs_p": "p.Arg79Lys",
"transcript": "ENST00000642566.2",
"protein_id": "ENSP00000496500.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 133,
"cds_start": 236,
"cds_end": null,
"cds_length": 402,
"cdna_start": 275,
"cdna_end": null,
"cdna_length": 551,
"mane_select": "NM_001395484.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.236G>A",
"hgvs_p": "p.Arg79Lys",
"transcript": "ENST00000326558.9",
"protein_id": "ENSP00000316012.5",
"transcript_support_level": 1,
"aa_start": 79,
"aa_end": null,
"aa_length": 108,
"cds_start": 236,
"cds_end": null,
"cds_length": 327,
"cdna_start": 259,
"cdna_end": null,
"cdna_length": 612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.312G>A",
"hgvs_p": "p.Ter104Ter",
"transcript": "ENST00000434307.6",
"protein_id": "ENSP00000416991.2",
"transcript_support_level": 1,
"aa_start": 104,
"aa_end": null,
"aa_length": 103,
"cds_start": 312,
"cds_end": null,
"cds_length": 312,
"cdna_start": 479,
"cdna_end": null,
"cdna_length": 777,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.215-2834G>A",
"hgvs_p": null,
"transcript": "ENST00000351436.8",
"protein_id": "ENSP00000297496.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 82,
"cds_start": -4,
"cds_end": null,
"cds_length": 249,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 534,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "n.152-1642G>A",
"hgvs_p": null,
"transcript": "ENST00000525884.1",
"protein_id": "ENSP00000434968.1",
"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": 552,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.236G>A",
"hgvs_p": "p.Arg79Lys",
"transcript": "NM_001081552.3",
"protein_id": "NP_001075021.2",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 108,
"cds_start": 236,
"cds_end": null,
"cds_length": 327,
"cdna_start": 275,
"cdna_end": null,
"cdna_length": 628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.77G>A",
"hgvs_p": "p.Arg26Lys",
"transcript": "ENST00000326625.5",
"protein_id": "ENSP00000316648.5",
"transcript_support_level": 5,
"aa_start": 26,
"aa_end": null,
"aa_length": 80,
"cds_start": 77,
"cds_end": null,
"cds_length": 243,
"cdna_start": 130,
"cdna_end": null,
"cdna_length": 445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.77G>A",
"hgvs_p": "p.Arg26Lys",
"transcript": "XM_017013744.2",
"protein_id": "XP_016869233.1",
"transcript_support_level": null,
"aa_start": 26,
"aa_end": null,
"aa_length": 80,
"cds_start": 77,
"cds_end": null,
"cds_length": 243,
"cdna_start": 77,
"cdna_end": null,
"cdna_length": 353,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.312G>A",
"hgvs_p": "p.Ter104Ter",
"transcript": "NM_001363726.3",
"protein_id": "NP_001350655.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 103,
"cds_start": 312,
"cds_end": null,
"cds_length": 312,
"cdna_start": 351,
"cdna_end": null,
"cdna_length": 627,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_retained_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.153G>A",
"hgvs_p": "p.Ter51Ter",
"transcript": "ENST00000454911.6",
"protein_id": "ENSP00000394885.2",
"transcript_support_level": 5,
"aa_start": 51,
"aa_end": null,
"aa_length": 50,
"cds_start": 153,
"cds_end": null,
"cds_length": 153,
"cdna_start": 206,
"cdna_end": null,
"cdna_length": 521,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": null,
"protein_coding": null,
"strand": true,
"consequences": [
"intragenic_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": null,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124901865",
"gene_hgnc_id": null,
"hgvs_c": "n.7860667G>A",
"hgvs_p": null,
"transcript": null,
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"hgvs_c": "c.161-7852G>A",
"hgvs_p": null,
"transcript": "ENST00000528033.3",
"protein_id": "ENSP00000436043.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 105,
"cds_start": -4,
"cds_end": null,
"cds_length": 318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPAG11A",
"gene_hgnc_id": 33342,
"dbsnp": "rs775284324",
"frequency_reference_population": 0.00014412313,
"hom_count_reference_population": 22,
"allele_count_reference_population": 219,
"gnomad_exomes_af": 0.000145113,
"gnomad_genomes_af": 0.000133927,
"gnomad_exomes_ac": 201,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 20,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000299602746963501,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": 0.212,
"revel_prediction": "Benign",
"alphamissense_score": 0.2036,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.071,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000642566.2",
"gene_symbol": "SPAG11A",
"hgnc_id": 33342,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.236G>A",
"hgvs_p": "p.Arg79Lys"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "",
"gene_symbol": "LOC124901865",
"hgnc_id": null,
"effects": [
"intragenic_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.7860667G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}