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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: 9-110785659-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=110785659&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 110785659,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000374448.9",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1719T>C",
"hgvs_p": "p.Asn573Asn",
"transcript": "NM_005592.4",
"protein_id": "NP_005583.1",
"transcript_support_level": null,
"aa_start": 573,
"aa_end": null,
"aa_length": 869,
"cds_start": 1719,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 1833,
"cdna_end": null,
"cdna_length": 8294,
"mane_select": "ENST00000374448.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1719T>C",
"hgvs_p": "p.Asn573Asn",
"transcript": "ENST00000374448.9",
"protein_id": "ENSP00000363571.4",
"transcript_support_level": 5,
"aa_start": 573,
"aa_end": null,
"aa_length": 869,
"cds_start": 1719,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 1833,
"cdna_end": null,
"cdna_length": 8294,
"mane_select": "NM_005592.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1695T>C",
"hgvs_p": "p.Asn565Asn",
"transcript": "ENST00000416899.7",
"protein_id": "ENSP00000393608.3",
"transcript_support_level": 5,
"aa_start": 565,
"aa_end": null,
"aa_length": 861,
"cds_start": 1695,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 1821,
"cdna_end": null,
"cdna_length": 3344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1461T>C",
"hgvs_p": "p.Asn487Asn",
"transcript": "NM_001166280.2",
"protein_id": "NP_001159752.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 783,
"cds_start": 1461,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 1575,
"cdna_end": null,
"cdna_length": 8036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1461T>C",
"hgvs_p": "p.Asn487Asn",
"transcript": "ENST00000189978.10",
"protein_id": "ENSP00000189978.6",
"transcript_support_level": 5,
"aa_start": 487,
"aa_end": null,
"aa_length": 783,
"cds_start": 1461,
"cds_end": null,
"cds_length": 2352,
"cdna_start": 1507,
"cdna_end": null,
"cdna_length": 2408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1431T>C",
"hgvs_p": "p.Asn477Asn",
"transcript": "NM_001166281.2",
"protein_id": "NP_001159753.1",
"transcript_support_level": null,
"aa_start": 477,
"aa_end": null,
"aa_length": 773,
"cds_start": 1431,
"cds_end": null,
"cds_length": 2322,
"cdna_start": 1545,
"cdna_end": null,
"cdna_length": 8006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.459T>C",
"hgvs_p": "p.Asn153Asn",
"transcript": "NM_001369398.1",
"protein_id": "NP_001356327.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 449,
"cds_start": 459,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1101,
"cdna_end": null,
"cdna_length": 7562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1749T>C",
"hgvs_p": "p.Asn583Asn",
"transcript": "XM_005251994.4",
"protein_id": "XP_005252051.1",
"transcript_support_level": null,
"aa_start": 583,
"aa_end": null,
"aa_length": 879,
"cds_start": 1749,
"cds_end": null,
"cds_length": 2640,
"cdna_start": 1863,
"cdna_end": null,
"cdna_length": 8324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1725T>C",
"hgvs_p": "p.Asn575Asn",
"transcript": "XM_005251995.4",
"protein_id": "XP_005252052.1",
"transcript_support_level": null,
"aa_start": 575,
"aa_end": null,
"aa_length": 871,
"cds_start": 1725,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 1839,
"cdna_end": null,
"cdna_length": 8300,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1695T>C",
"hgvs_p": "p.Asn565Asn",
"transcript": "XM_005251996.4",
"protein_id": "XP_005252053.1",
"transcript_support_level": null,
"aa_start": 565,
"aa_end": null,
"aa_length": 861,
"cds_start": 1695,
"cds_end": null,
"cds_length": 2586,
"cdna_start": 1809,
"cdna_end": null,
"cdna_length": 8270,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.1485T>C",
"hgvs_p": "p.Asn495Asn",
"transcript": "XM_017014734.2",
"protein_id": "XP_016870223.1",
"transcript_support_level": null,
"aa_start": 495,
"aa_end": null,
"aa_length": 791,
"cds_start": 1485,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 1599,
"cdna_end": null,
"cdna_length": 8060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "c.483T>C",
"hgvs_p": "p.Asn161Asn",
"transcript": "XM_011518708.3",
"protein_id": "XP_011517010.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 457,
"cds_start": 483,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 598,
"cdna_end": null,
"cdna_length": 7059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "MUSK",
"gene_hgnc_id": 7525,
"hgvs_c": "n.750T>C",
"hgvs_p": null,
"transcript": "ENST00000374438.1",
"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": 1221,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC107987115",
"gene_hgnc_id": null,
"hgvs_c": "n.33A>G",
"hgvs_p": null,
"transcript": "XR_001746892.2",
"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": 4037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MUSK",
"gene_hgnc_id": 7525,
"dbsnp": "rs373118888",
"frequency_reference_population": 0.0010278614,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1658,
"gnomad_exomes_af": 0.00106849,
"gnomad_genomes_af": 0.00063768,
"gnomad_exomes_ac": 1561,
"gnomad_genomes_ac": 97,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"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": 0.009999999776482582,
"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": 1.123,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000374448.9",
"gene_symbol": "MUSK",
"hgnc_id": 7525,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1719T>C",
"hgvs_p": "p.Asn573Asn"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "XR_001746892.2",
"gene_symbol": "LOC107987115",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.33A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital myasthenic syndrome 9,Fetal akinesia deformation sequence 1,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "not specified|Fetal akinesia deformation sequence 1;Congenital myasthenic syndrome 9|Congenital myasthenic syndrome 9",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}