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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: 11-68439808-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=68439808&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 68439808,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000294304.12",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4380C>T",
"hgvs_p": "p.Ser1460Ser",
"transcript": "NM_002335.4",
"protein_id": "NP_002326.2",
"transcript_support_level": null,
"aa_start": 1460,
"aa_end": null,
"aa_length": 1615,
"cds_start": 4380,
"cds_end": null,
"cds_length": 4848,
"cdna_start": 4504,
"cdna_end": null,
"cdna_length": 5177,
"mane_select": "ENST00000294304.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4380C>T",
"hgvs_p": "p.Ser1460Ser",
"transcript": "ENST00000294304.12",
"protein_id": "ENSP00000294304.6",
"transcript_support_level": 1,
"aa_start": 1460,
"aa_end": null,
"aa_length": 1615,
"cds_start": 4380,
"cds_end": null,
"cds_length": 4848,
"cdna_start": 4504,
"cdna_end": null,
"cdna_length": 5177,
"mane_select": "NM_002335.4",
"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": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "n.*2986C>T",
"hgvs_p": null,
"transcript": "ENST00000529993.5",
"protein_id": "ENSP00000436652.1",
"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": 5103,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "n.*2986C>T",
"hgvs_p": null,
"transcript": "ENST00000529993.5",
"protein_id": "ENSP00000436652.1",
"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": 5103,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.2637C>T",
"hgvs_p": "p.Ser879Ser",
"transcript": "NM_001291902.2",
"protein_id": "NP_001278831.1",
"transcript_support_level": null,
"aa_start": 879,
"aa_end": null,
"aa_length": 1034,
"cds_start": 2637,
"cds_end": null,
"cds_length": 3105,
"cdna_start": 4526,
"cdna_end": null,
"cdna_length": 5199,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4407C>T",
"hgvs_p": "p.Ser1469Ser",
"transcript": "XM_011545029.2",
"protein_id": "XP_011543331.1",
"transcript_support_level": null,
"aa_start": 1469,
"aa_end": null,
"aa_length": 1662,
"cds_start": 4407,
"cds_end": null,
"cds_length": 4989,
"cdna_start": 4876,
"cdna_end": null,
"cdna_length": 5663,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4380C>T",
"hgvs_p": "p.Ser1460Ser",
"transcript": "XM_005273994.3",
"protein_id": "XP_005274051.1",
"transcript_support_level": null,
"aa_start": 1460,
"aa_end": null,
"aa_length": 1653,
"cds_start": 4380,
"cds_end": null,
"cds_length": 4962,
"cdna_start": 4504,
"cdna_end": null,
"cdna_length": 5291,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4407C>T",
"hgvs_p": "p.Ser1469Ser",
"transcript": "XM_011545030.2",
"protein_id": "XP_011543332.1",
"transcript_support_level": null,
"aa_start": 1469,
"aa_end": null,
"aa_length": 1624,
"cds_start": 4407,
"cds_end": null,
"cds_length": 4875,
"cdna_start": 4876,
"cdna_end": null,
"cdna_length": 5549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4407C>T",
"hgvs_p": "p.Ser1469Ser",
"transcript": "XM_011545031.2",
"protein_id": "XP_011543333.1",
"transcript_support_level": null,
"aa_start": 1469,
"aa_end": null,
"aa_length": 1600,
"cds_start": 4407,
"cds_end": null,
"cds_length": 4803,
"cdna_start": 4876,
"cdna_end": null,
"cdna_length": 5679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4407C>T",
"hgvs_p": "p.Ser1469Ser",
"transcript": "XM_047426948.1",
"protein_id": "XP_047282904.1",
"transcript_support_level": null,
"aa_start": 1469,
"aa_end": null,
"aa_length": 1594,
"cds_start": 4407,
"cds_end": null,
"cds_length": 4785,
"cdna_start": 4876,
"cdna_end": null,
"cdna_length": 5427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4407C>T",
"hgvs_p": "p.Ser1469Ser",
"transcript": "XM_047426949.1",
"protein_id": "XP_047282905.1",
"transcript_support_level": null,
"aa_start": 1469,
"aa_end": null,
"aa_length": 1586,
"cds_start": 4407,
"cds_end": null,
"cds_length": 4761,
"cdna_start": 4876,
"cdna_end": null,
"cdna_length": 5443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.4407C>T",
"hgvs_p": "p.Ser1469Ser",
"transcript": "XM_047426950.1",
"protein_id": "XP_047282906.1",
"transcript_support_level": null,
"aa_start": 1469,
"aa_end": null,
"aa_length": 1556,
"cds_start": 4407,
"cds_end": null,
"cds_length": 4671,
"cdna_start": 4876,
"cdna_end": null,
"cdna_length": 5313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.2637C>T",
"hgvs_p": "p.Ser879Ser",
"transcript": "XM_017017735.2",
"protein_id": "XP_016873224.1",
"transcript_support_level": null,
"aa_start": 879,
"aa_end": null,
"aa_length": 1072,
"cds_start": 2637,
"cds_end": null,
"cds_length": 3219,
"cdna_start": 2714,
"cdna_end": null,
"cdna_length": 3501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.1920C>T",
"hgvs_p": "p.Ser640Ser",
"transcript": "XM_017017736.2",
"protein_id": "XP_016873225.1",
"transcript_support_level": null,
"aa_start": 640,
"aa_end": null,
"aa_length": 833,
"cds_start": 1920,
"cds_end": null,
"cds_length": 2502,
"cdna_start": 2081,
"cdna_end": null,
"cdna_length": 2868,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "n.122C>T",
"hgvs_p": null,
"transcript": "ENST00000533695.1",
"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": 267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"hgvs_c": "c.-67C>T",
"hgvs_p": null,
"transcript": "ENST00000529702.1",
"protein_id": "ENSP00000435315.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 171,
"cds_start": -4,
"cds_end": null,
"cds_length": 516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LRP5",
"gene_hgnc_id": 6697,
"dbsnp": "rs11574420",
"frequency_reference_population": 0.0022602368,
"hom_count_reference_population": 10,
"allele_count_reference_population": 3643,
"gnomad_exomes_af": 0.00231862,
"gnomad_genomes_af": 0.00170072,
"gnomad_exomes_ac": 3384,
"gnomad_genomes_ac": 259,
"gnomad_exomes_homalt": 10,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3700000047683716,
"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": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.632,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000294304.12",
"gene_symbol": "LRP5",
"hgnc_id": 6697,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR,SD,Unknown",
"hgvs_c": "c.4380C>T",
"hgvs_p": "p.Ser1460Ser"
}
],
"clinvar_disease": "8 conditions,Osteogenesis imperfecta,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:2",
"phenotype_combined": "not specified|not provided|Osteogenesis imperfecta|8 conditions",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}