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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: 2-188993438-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=188993438&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 15,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "COL3A1",
"hgnc_id": 2201,
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -15,
"transcript": "NM_000090.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1",
"acmg_score": -15,
"allele_count_reference_population": 100,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"chr": "2",
"clinvar_classification": "Likely benign",
"clinvar_disease": " type 4,COL3A1-related disorder,Connective tissue disorder,Ehlers-Danlos syndrome,Familial thoracic aortic aneurysm and aortic dissection,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:6",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.3499999940395355,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1466,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5490,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4401,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 51,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_000090.4",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000304636.9",
"protein_coding": true,
"protein_id": "NP_000081.2",
"strand": true,
"transcript": "NM_000090.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1466,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5490,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4401,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 51,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000304636.9",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000090.4",
"protein_coding": true,
"protein_id": "ENSP00000304408.4",
"strand": true,
"transcript": "ENST00000304636.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1433,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5391,
"cdna_start": null,
"cds_end": null,
"cds_length": 4302,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 50,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000450867.2",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1050+498C>T",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000415346.2",
"strand": true,
"transcript": "ENST00000450867.2",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "H",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4787,
"cdna_start": 1236,
"cds_end": null,
"cds_length": 4392,
"cds_start": 1119,
"consequences": [
"synonymous_variant"
],
"exon_count": 51,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000879201.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1119C>T",
"hgvs_p": "p.His373His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549260.1",
"strand": true,
"transcript": "ENST00000879201.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1451,
"aa_ref": "H",
"aa_start": 361,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4757,
"cdna_start": 1200,
"cds_end": null,
"cds_length": 4356,
"cds_start": 1083,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000879198.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1083C>T",
"hgvs_p": "p.His361His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549257.1",
"strand": true,
"transcript": "ENST00000879198.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1449,
"aa_ref": "H",
"aa_start": 359,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5436,
"cdna_start": 1194,
"cds_end": null,
"cds_length": 4350,
"cds_start": 1077,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000879194.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1077C>T",
"hgvs_p": "p.His359His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549253.1",
"strand": true,
"transcript": "ENST00000879194.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4742,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4347,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000879200.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549259.1",
"strand": true,
"transcript": "ENST00000879200.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4669,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4347,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000879202.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549261.1",
"strand": true,
"transcript": "ENST00000879202.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4743,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4347,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000957918.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627977.1",
"strand": true,
"transcript": "ENST00000957918.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1433,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5388,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4302,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000879195.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549254.1",
"strand": true,
"transcript": "ENST00000879195.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1430,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5376,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4293,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000879196.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549255.1",
"strand": true,
"transcript": "ENST00000879196.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1430,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5349,
"cdna_start": 1214,
"cds_end": null,
"cds_length": 4293,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000879197.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549256.1",
"strand": true,
"transcript": "ENST00000879197.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1430,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5382,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4293,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000957916.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627975.1",
"strand": true,
"transcript": "ENST00000957916.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1426,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5369,
"cdna_start": 1247,
"cds_end": null,
"cds_length": 4281,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 51,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000957917.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627976.1",
"strand": true,
"transcript": "ENST00000957917.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1425,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4428,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4278,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000879203.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549262.1",
"strand": true,
"transcript": "ENST00000879203.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1415,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5337,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4248,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 49,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000713745.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519049.1",
"strand": true,
"transcript": "ENST00000713745.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1412,
"aa_ref": "H",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5328,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 4239,
"cds_start": 1128,
"consequences": [
"synonymous_variant"
],
"exon_count": 49,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000713744.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1128C>T",
"hgvs_p": "p.His376His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519048.1",
"strand": true,
"transcript": "ENST00000713744.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1418,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4655,
"cdna_start": null,
"cds_end": null,
"cds_length": 4257,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 49,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000879199.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.1050+498C>T",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549258.1",
"strand": true,
"transcript": "ENST00000879199.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs771015742",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00006424588,
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"gnomad_exomes_ac": 92,
"gnomad_exomes_af": 0.0000654993,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 8,
"gnomad_genomes_af": 0.0000526579,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Ehlers-Danlos syndrome, type 4|Familial thoracic aortic aneurysm and aortic dissection|Connective tissue disorder|not provided|COL3A1-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.428,
"pos": 188993438,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000090.4"
}
]
}