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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: 2-189010711-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189010711&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PP2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL3A1",
"hgnc_id": 2201,
"hgvs_c": "c.4075C>A",
"hgvs_p": "p.Leu1359Ile",
"inheritance_mode": "AD,AR",
"pathogenic_score": 1,
"score": 0,
"transcript": "NM_000090.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2,BP4",
"acmg_score": 0,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": 0.1287,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.33,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " type 4,Ehlers-Danlos syndrome,Familial thoracic aortic aneurysm and aortic dissection",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.4169430434703827,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 1466,
"aa_ref": "L",
"aa_start": 1359,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5490,
"cdna_start": 4192,
"cds_end": null,
"cds_length": 4401,
"cds_start": 4075,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 50,
"exon_rank_end": null,
"feature": "NM_000090.4",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.4075C>A",
"hgvs_p": "p.Leu1359Ile",
"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": "I",
"aa_end": null,
"aa_length": 1466,
"aa_ref": "L",
"aa_start": 1359,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5490,
"cdna_start": 4192,
"cds_end": null,
"cds_length": 4401,
"cds_start": 4075,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 50,
"exon_rank_end": null,
"feature": "ENST00000304636.9",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.4075C>A",
"hgvs_p": "p.Leu1359Ile",
"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": "I",
"aa_end": null,
"aa_length": 1433,
"aa_ref": "L",
"aa_start": 1326,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5391,
"cdna_start": 4093,
"cds_end": null,
"cds_length": 4302,
"cds_start": 3976,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000450867.2",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3976C>A",
"hgvs_p": "p.Leu1326Ile",
"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": "I",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "L",
"aa_start": 1356,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4787,
"cdna_start": 4183,
"cds_end": null,
"cds_length": 4392,
"cds_start": 4066,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 50,
"exon_rank_end": null,
"feature": "ENST00000879201.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.4066C>A",
"hgvs_p": "p.Leu1356Ile",
"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": "I",
"aa_end": null,
"aa_length": 1451,
"aa_ref": "L",
"aa_start": 1344,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4757,
"cdna_start": 4147,
"cds_end": null,
"cds_length": 4356,
"cds_start": 4030,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000879198.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.4030C>A",
"hgvs_p": "p.Leu1344Ile",
"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": "I",
"aa_end": null,
"aa_length": 1449,
"aa_ref": "L",
"aa_start": 1342,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5436,
"cdna_start": 4141,
"cds_end": null,
"cds_length": 4350,
"cds_start": 4024,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000879194.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.4024C>A",
"hgvs_p": "p.Leu1342Ile",
"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": "I",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "L",
"aa_start": 1341,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4742,
"cdna_start": 4138,
"cds_end": null,
"cds_length": 4347,
"cds_start": 4021,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000879200.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.4021C>A",
"hgvs_p": "p.Leu1341Ile",
"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": "I",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "L",
"aa_start": 1341,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4669,
"cdna_start": 4138,
"cds_end": null,
"cds_length": 4347,
"cds_start": 4021,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000879202.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.4021C>A",
"hgvs_p": "p.Leu1341Ile",
"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": "I",
"aa_end": null,
"aa_length": 1448,
"aa_ref": "L",
"aa_start": 1341,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4743,
"cdna_start": 4138,
"cds_end": null,
"cds_length": 4347,
"cds_start": 4021,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000957918.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.4021C>A",
"hgvs_p": "p.Leu1341Ile",
"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": "I",
"aa_end": null,
"aa_length": 1433,
"aa_ref": "L",
"aa_start": 1326,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5388,
"cdna_start": 4093,
"cds_end": null,
"cds_length": 4302,
"cds_start": 3976,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000879195.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3976C>A",
"hgvs_p": "p.Leu1326Ile",
"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": "I",
"aa_end": null,
"aa_length": 1430,
"aa_ref": "L",
"aa_start": 1323,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5376,
"cdna_start": 4084,
"cds_end": null,
"cds_length": 4293,
"cds_start": 3967,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000879196.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3967C>A",
"hgvs_p": "p.Leu1323Ile",
"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": "I",
"aa_end": null,
"aa_length": 1430,
"aa_ref": "L",
"aa_start": 1323,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5349,
"cdna_start": 4053,
"cds_end": null,
"cds_length": 4293,
"cds_start": 3967,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000879197.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3967C>A",
"hgvs_p": "p.Leu1323Ile",
"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": "I",
"aa_end": null,
"aa_length": 1430,
"aa_ref": "L",
"aa_start": 1323,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5382,
"cdna_start": 4084,
"cds_end": null,
"cds_length": 4293,
"cds_start": 3967,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000957916.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3967C>A",
"hgvs_p": "p.Leu1323Ile",
"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": "I",
"aa_end": null,
"aa_length": 1426,
"aa_ref": "L",
"aa_start": 1319,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5369,
"cdna_start": 4074,
"cds_end": null,
"cds_length": 4281,
"cds_start": 3955,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 50,
"exon_rank_end": null,
"feature": "ENST00000957917.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3955C>A",
"hgvs_p": "p.Leu1319Ile",
"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": "I",
"aa_end": null,
"aa_length": 1425,
"aa_ref": "L",
"aa_start": 1318,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4428,
"cdna_start": 4069,
"cds_end": null,
"cds_length": 4278,
"cds_start": 3952,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 49,
"exon_rank_end": null,
"feature": "ENST00000879203.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3952C>A",
"hgvs_p": "p.Leu1318Ile",
"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": "I",
"aa_end": null,
"aa_length": 1418,
"aa_ref": "L",
"aa_start": 1311,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4655,
"cdna_start": 4048,
"cds_end": null,
"cds_length": 4257,
"cds_start": 3931,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000879199.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3931C>A",
"hgvs_p": "p.Leu1311Ile",
"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": "I",
"aa_end": null,
"aa_length": 1415,
"aa_ref": "L",
"aa_start": 1308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5337,
"cdna_start": 4039,
"cds_end": null,
"cds_length": 4248,
"cds_start": 3922,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000713745.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3922C>A",
"hgvs_p": "p.Leu1308Ile",
"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": "I",
"aa_end": null,
"aa_length": 1412,
"aa_ref": "L",
"aa_start": 1305,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5328,
"cdna_start": 4030,
"cds_end": null,
"cds_length": 4239,
"cds_start": 3913,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000713744.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "c.3913C>A",
"hgvs_p": "p.Leu1305Ile",
"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": 2,
"exon_rank_end": null,
"feature": "ENST00000487010.1",
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"hgvs_c": "n.1454C>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": "ENST00000487010.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1400489265",
"effect": "missense_variant",
"frequency_reference_population": 0.0000043369273,
"gene_hgnc_id": 2201,
"gene_symbol": "COL3A1",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136814,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328502,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Ehlers-Danlos syndrome, type 4|Familial thoracic aortic aneurysm and aortic dissection",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.078,
"pos": 189010711,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.329,
"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"
}
]
}