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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: 5-13776662-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13776662&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 13776662,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000265104.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9150C>T",
"hgvs_p": "p.Ser3050Ser",
"transcript": "NM_001369.3",
"protein_id": "NP_001360.1",
"transcript_support_level": null,
"aa_start": 3050,
"aa_end": null,
"aa_length": 4624,
"cds_start": 9150,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 9400,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "ENST00000265104.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9150C>T",
"hgvs_p": "p.Ser3050Ser",
"transcript": "ENST00000265104.5",
"protein_id": "ENSP00000265104.4",
"transcript_support_level": 1,
"aa_start": 3050,
"aa_end": null,
"aa_length": 4624,
"cds_start": 9150,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 9400,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "NM_001369.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9105C>T",
"hgvs_p": "p.Ser3035Ser",
"transcript": "ENST00000681290.1",
"protein_id": "ENSP00000505288.1",
"transcript_support_level": null,
"aa_start": 3035,
"aa_end": null,
"aa_length": 4609,
"cds_start": 9105,
"cds_end": null,
"cds_length": 13830,
"cdna_start": 9264,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9258C>T",
"hgvs_p": "p.Ser3086Ser",
"transcript": "XM_005248262.4",
"protein_id": "XP_005248319.2",
"transcript_support_level": null,
"aa_start": 3086,
"aa_end": null,
"aa_length": 4660,
"cds_start": 9258,
"cds_end": null,
"cds_length": 13983,
"cdna_start": 9264,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.8910C>T",
"hgvs_p": "p.Ser2970Ser",
"transcript": "XM_047416886.1",
"protein_id": "XP_047272842.1",
"transcript_support_level": null,
"aa_start": 2970,
"aa_end": null,
"aa_length": 4544,
"cds_start": 8910,
"cds_end": null,
"cds_length": 13635,
"cdna_start": 10029,
"cdna_end": null,
"cdna_length": 16410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 77,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9258C>T",
"hgvs_p": "p.Ser3086Ser",
"transcript": "XM_017009177.2",
"protein_id": "XP_016864666.1",
"transcript_support_level": null,
"aa_start": 3086,
"aa_end": null,
"aa_length": 4520,
"cds_start": 9258,
"cds_end": null,
"cds_length": 13563,
"cdna_start": 9264,
"cdna_end": null,
"cdna_length": 15225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.8163C>T",
"hgvs_p": "p.Ser2721Ser",
"transcript": "XM_017009179.3",
"protein_id": "XP_016864668.1",
"transcript_support_level": null,
"aa_start": 2721,
"aa_end": null,
"aa_length": 4295,
"cds_start": 8163,
"cds_end": null,
"cds_length": 12888,
"cdna_start": 8372,
"cdna_end": null,
"cdna_length": 14753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 74,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9258C>T",
"hgvs_p": "p.Ser3086Ser",
"transcript": "XM_017009180.2",
"protein_id": "XP_016864669.1",
"transcript_support_level": null,
"aa_start": 3086,
"aa_end": null,
"aa_length": 4272,
"cds_start": 9258,
"cds_end": null,
"cds_length": 12819,
"cdna_start": 9264,
"cdna_end": null,
"cdna_length": 12932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9258C>T",
"hgvs_p": "p.Ser3086Ser",
"transcript": "XM_017009181.2",
"protein_id": "XP_016864670.1",
"transcript_support_level": null,
"aa_start": 3086,
"aa_end": null,
"aa_length": 3960,
"cds_start": 9258,
"cds_end": null,
"cds_length": 11883,
"cdna_start": 9264,
"cdna_end": null,
"cdna_length": 11987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 55,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9258C>T",
"hgvs_p": "p.Ser3086Ser",
"transcript": "XM_017009182.2",
"protein_id": "XP_016864671.1",
"transcript_support_level": null,
"aa_start": 3086,
"aa_end": null,
"aa_length": 3809,
"cds_start": 9258,
"cds_end": null,
"cds_length": 11430,
"cdna_start": 9264,
"cdna_end": null,
"cdna_length": 11526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.4347C>T",
"hgvs_p": "p.Ser1449Ser",
"transcript": "XM_017009185.1",
"protein_id": "XP_016864674.1",
"transcript_support_level": null,
"aa_start": 1449,
"aa_end": null,
"aa_length": 3023,
"cds_start": 4347,
"cds_end": null,
"cds_length": 9072,
"cdna_start": 4571,
"cdna_end": null,
"cdna_length": 10952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.3900C>T",
"hgvs_p": "p.Ser1300Ser",
"transcript": "XM_017009186.2",
"protein_id": "XP_016864675.1",
"transcript_support_level": null,
"aa_start": 1300,
"aa_end": null,
"aa_length": 2874,
"cds_start": 3900,
"cds_end": null,
"cds_length": 8625,
"cdna_start": 4002,
"cdna_end": null,
"cdna_length": 10383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.3237C>T",
"hgvs_p": "p.Ser1079Ser",
"transcript": "XM_017009188.2",
"protein_id": "XP_016864677.1",
"transcript_support_level": null,
"aa_start": 1079,
"aa_end": null,
"aa_length": 2653,
"cds_start": 3237,
"cds_end": null,
"cds_length": 7962,
"cdna_start": 4804,
"cdna_end": null,
"cdna_length": 11185,
"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": 54,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.9133C>T",
"hgvs_p": null,
"transcript": "XR_001742034.2",
"protein_id": null,
"transcript_support_level": null,
"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": 9175,
"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": 54,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.9128C>T",
"hgvs_p": null,
"transcript": "XR_001742035.2",
"protein_id": null,
"transcript_support_level": null,
"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": 9166,
"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": 55,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.*37C>T",
"hgvs_p": null,
"transcript": "XM_017009184.2",
"protein_id": "XP_016864673.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3071,
"cds_start": -4,
"cds_end": null,
"cds_length": 9216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"dbsnp": "rs77477793",
"frequency_reference_population": 0.00087871065,
"hom_count_reference_population": 18,
"allele_count_reference_population": 1418,
"gnomad_exomes_af": 0.000458421,
"gnomad_genomes_af": 0.00491491,
"gnomad_exomes_ac": 670,
"gnomad_genomes_ac": 748,
"gnomad_exomes_homalt": 9,
"gnomad_genomes_homalt": 9,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.352,
"phylop100way_prediction": "Benign",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000265104.5",
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.9150C>T",
"hgvs_p": "p.Ser3050Ser"
}
],
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 3,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:3",
"phenotype_combined": "not specified|Primary ciliary dyskinesia|Primary ciliary dyskinesia 3",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}