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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: 2-189009172-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189009172&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 17,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "COL3A1",
"hgnc_id": 2201,
"hgvs_c": "c.3774C>T",
"hgvs_p": "p.Pro1258Pro",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -17,
"transcript": "NM_000090.4",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000295704",
"hgnc_id": null,
"hgvs_c": "n.-100G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000731902.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1",
"acmg_score": -17,
"allele_count_reference_population": 147,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.52,
"chr": "2",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": " type 4,COL3A1-related 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:4 B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5199999809265137,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1466,
"aa_ref": "P",
"aa_start": 1258,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5490,
"cdna_start": 3891,
"cds_end": null,
"cds_length": 4401,
"cds_start": 3774,
"consequences": [
"synonymous_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "NM_000090.4",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3774C>T",
"hgvs_p": "p.Pro1258Pro",
"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": "P",
"aa_end": null,
"aa_length": 1466,
"aa_ref": "P",
"aa_start": 1258,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5490,
"cdna_start": 3891,
"cds_end": null,
"cds_length": 4401,
"cds_start": 3774,
"consequences": [
"synonymous_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000304636.9",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3774C>T",
"hgvs_p": "p.Pro1258Pro",
"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": "P",
"aa_end": null,
"aa_length": 1433,
"aa_ref": "P",
"aa_start": 1225,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5391,
"cdna_start": 3792,
"cds_end": null,
"cds_length": 4302,
"cds_start": 3675,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000450867.2",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3675C>T",
"hgvs_p": "p.Pro1225Pro",
"intron_rank": null,
"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": "P",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "P",
"aa_start": 1255,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4787,
"cdna_start": 3882,
"cds_end": null,
"cds_length": 4392,
"cds_start": 3765,
"consequences": [
"synonymous_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000879201.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3765C>T",
"hgvs_p": "p.Pro1255Pro",
"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": "P",
"aa_end": null,
"aa_length": 1451,
"aa_ref": "P",
"aa_start": 1243,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4757,
"cdna_start": 3846,
"cds_end": null,
"cds_length": 4356,
"cds_start": 3729,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000879198.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3729C>T",
"hgvs_p": "p.Pro1243Pro",
"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": "P",
"aa_end": null,
"aa_length": 1449,
"aa_ref": "P",
"aa_start": 1241,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5436,
"cdna_start": 3840,
"cds_end": null,
"cds_length": 4350,
"cds_start": 3723,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000879194.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3723C>T",
"hgvs_p": "p.Pro1241Pro",
"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": "P",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "P",
"aa_start": 1240,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4742,
"cdna_start": 3837,
"cds_end": null,
"cds_length": 4347,
"cds_start": 3720,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000879200.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3720C>T",
"hgvs_p": "p.Pro1240Pro",
"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": "P",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "P",
"aa_start": 1240,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4669,
"cdna_start": 3837,
"cds_end": null,
"cds_length": 4347,
"cds_start": 3720,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000879202.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3720C>T",
"hgvs_p": "p.Pro1240Pro",
"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": "P",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "P",
"aa_start": 1240,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4743,
"cdna_start": 3837,
"cds_end": null,
"cds_length": 4347,
"cds_start": 3720,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000957918.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3720C>T",
"hgvs_p": "p.Pro1240Pro",
"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": "P",
"aa_end": null,
"aa_length": 1433,
"aa_ref": "P",
"aa_start": 1225,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5388,
"cdna_start": 3792,
"cds_end": null,
"cds_length": 4302,
"cds_start": 3675,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000879195.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3675C>T",
"hgvs_p": "p.Pro1225Pro",
"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": "P",
"aa_end": null,
"aa_length": 1430,
"aa_ref": "P",
"aa_start": 1222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5376,
"cdna_start": 3783,
"cds_end": null,
"cds_length": 4293,
"cds_start": 3666,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000879196.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3666C>T",
"hgvs_p": "p.Pro1222Pro",
"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": "P",
"aa_end": null,
"aa_length": 1430,
"aa_ref": "P",
"aa_start": 1222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5349,
"cdna_start": 3752,
"cds_end": null,
"cds_length": 4293,
"cds_start": 3666,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000879197.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3666C>T",
"hgvs_p": "p.Pro1222Pro",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549256.1",
"strand": true,
"transcript": "ENST00000879197.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
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"aa_ref": "P",
"aa_start": 1222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5382,
"cdna_start": 3783,
"cds_end": null,
"cds_length": 4293,
"cds_start": 3666,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000957916.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3666C>T",
"hgvs_p": "p.Pro1222Pro",
"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": "P",
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"aa_length": 1426,
"aa_ref": "P",
"aa_start": 1218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5369,
"cdna_start": 3773,
"cds_end": null,
"cds_length": 4281,
"cds_start": 3654,
"consequences": [
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],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000957917.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3654C>T",
"hgvs_p": "p.Pro1218Pro",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627976.1",
"strand": true,
"transcript": "ENST00000957917.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1425,
"aa_ref": "P",
"aa_start": 1217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4428,
"cdna_start": 3768,
"cds_end": null,
"cds_length": 4278,
"cds_start": 3651,
"consequences": [
"synonymous_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000879203.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3651C>T",
"hgvs_p": "p.Pro1217Pro",
"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": "P",
"aa_end": null,
"aa_length": 1418,
"aa_ref": "P",
"aa_start": 1210,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4655,
"cdna_start": 3747,
"cds_end": null,
"cds_length": 4257,
"cds_start": 3630,
"consequences": [
"synonymous_variant"
],
"exon_count": 49,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "ENST00000879199.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3630C>T",
"hgvs_p": "p.Pro1210Pro",
"intron_rank": null,
"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
},
{
"aa_alt": "P",
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"aa_length": 1415,
"aa_ref": "P",
"aa_start": 1207,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5337,
"cdna_start": 3738,
"cds_end": null,
"cds_length": 4248,
"cds_start": 3621,
"consequences": [
"synonymous_variant"
],
"exon_count": 49,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "ENST00000713745.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3621C>T",
"hgvs_p": "p.Pro1207Pro",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519049.1",
"strand": true,
"transcript": "ENST00000713745.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1412,
"aa_ref": "P",
"aa_start": 1204,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5328,
"cdna_start": 3729,
"cds_end": null,
"cds_length": 4239,
"cds_start": 3612,
"consequences": [
"synonymous_variant"
],
"exon_count": 49,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "ENST00000713744.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3612C>T",
"hgvs_p": "p.Pro1204Pro",
"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": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2054,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000487010.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "n.871C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000487010.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 439,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000731902.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000295704",
"hgvs_c": "n.-100G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000731902.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs149790711",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00009107536,
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"gnomad_exomes_ac": 80,
"gnomad_exomes_af": 0.0000547242,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 67,
"gnomad_genomes_af": 0.000440291,
"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": "Benign/Likely benign",
"phenotype_combined": "Ehlers-Danlos syndrome, type 4|not provided|Familial thoracic aortic aneurysm and aortic dissection|COL3A1-related disorder",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.534,
"pos": 189009172,
"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"
}
]
}