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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: 21-45505438-GTC-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=45505438&ref=GTC&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 45505438,
"ref": "GTC",
"alt": "G",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000651438.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"hgvs_c": "c.3087+9_3087+10delCT",
"hgvs_p": null,
"transcript": "NM_001379500.1",
"protein_id": "NP_001366429.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1339,
"cds_start": -4,
"cds_end": null,
"cds_length": 4020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5408,
"mane_select": "ENST00000651438.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": 36,
"intron_rank_end": null,
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"hgvs_c": "c.3087+8_3087+9delTC",
"hgvs_p": null,
"transcript": "ENST00000651438.1",
"protein_id": "ENSP00000498485.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1339,
"cds_start": -4,
"cds_end": null,
"cds_length": 4020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5408,
"mane_select": "NM_001379500.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"hgvs_c": "c.3627+8_3627+9delTC",
"hgvs_p": null,
"transcript": "ENST00000355480.10",
"protein_id": "ENSP00000347665.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1519,
"cds_start": -4,
"cds_end": null,
"cds_length": 4560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SLC19A1",
"gene_hgnc_id": 10937,
"hgvs_c": "c.1294-6828_1294-6827delGA",
"hgvs_p": null,
"transcript": "ENST00000567670.5",
"protein_id": "ENSP00000457278.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 545,
"cds_start": -4,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2029,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC19A1",
"gene_hgnc_id": 10937,
"hgvs_c": "c.496-6828_496-6827delGA",
"hgvs_p": null,
"transcript": "ENST00000417954.5",
"protein_id": "ENSP00000393988.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 268,
"cds_start": -4,
"cds_end": null,
"cds_length": 807,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"hgvs_c": "c.4332+9_4332+10delCT",
"hgvs_p": null,
"transcript": "NM_130444.3",
"protein_id": "NP_569711.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1754,
"cds_start": -4,
"cds_end": null,
"cds_length": 5265,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"hgvs_c": "c.4332+8_4332+9delTC",
"hgvs_p": null,
"transcript": "ENST00000359759.8",
"protein_id": "ENSP00000352798.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1754,
"cds_start": -4,
"cds_end": null,
"cds_length": 5265,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"hgvs_c": "c.3627+9_3627+10delCT",
"hgvs_p": null,
"transcript": "NM_030582.4",
"protein_id": "NP_085059.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1519,
"cds_start": -4,
"cds_end": null,
"cds_length": 4560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"hgvs_c": "c.1128+8_1128+9delTC",
"hgvs_p": null,
"transcript": "ENST00000342220.9",
"protein_id": "ENSP00000339118.5",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 687,
"cds_start": -4,
"cds_end": null,
"cds_length": 2064,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"hgvs_c": "c.72+8_72+9delTC",
"hgvs_p": null,
"transcript": "ENST00000423214.1",
"protein_id": "ENSP00000415692.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 278,
"cds_start": -4,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SLC19A1",
"gene_hgnc_id": 10937,
"hgvs_c": "c.1360-2471_1360-2470delGA",
"hgvs_p": null,
"transcript": "XM_047440957.1",
"protein_id": "XP_047296913.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 466,
"cds_start": -4,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SLC19A1",
"gene_hgnc_id": 10937,
"hgvs_c": "c.1294-2471_1294-2470delGA",
"hgvs_p": null,
"transcript": "XM_047440963.1",
"protein_id": "XP_047296919.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 444,
"cds_start": -4,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SLC19A1",
"gene_hgnc_id": 10937,
"hgvs_c": "c.1294-2471_1294-2470delGA",
"hgvs_p": null,
"transcript": "XM_047440964.1",
"protein_id": "XP_047296920.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 444,
"cds_start": -4,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL18A1",
"gene_hgnc_id": 2195,
"dbsnp": "rs373823632",
"frequency_reference_population": 0.01661597,
"hom_count_reference_population": 341,
"allele_count_reference_population": 25106,
"gnomad_exomes_af": 0.0163346,
"gnomad_genomes_af": 0.0191257,
"gnomad_exomes_ac": 22193,
"gnomad_genomes_ac": 2913,
"gnomad_exomes_homalt": 291,
"gnomad_genomes_homalt": 50,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"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": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -0.246,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000651438.1",
"gene_symbol": "COL18A1",
"hgnc_id": 2195,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3087+8_3087+9delTC",
"hgvs_p": null
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000567670.5",
"gene_symbol": "SLC19A1",
"hgnc_id": 10937,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1294-6828_1294-6827delGA",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}