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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: 12-47982158-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=47982158&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7"
],
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"gene_symbol": "COL2A1",
"hgnc_id": 2200,
"hgvs_c": "c.2304T>C",
"hgvs_p": "p.Gly768Gly",
"inheritance_mode": "AD,AR,Unknown",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_001844.5",
"verdict": "Likely_benign"
},
{
"benign_score": 3,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC105369752",
"hgnc_id": null,
"hgvs_c": "n.219-257A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -1,
"transcript": "XR_944910.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7",
"acmg_score": -4,
"allele_count_reference_population": 10,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.4,
"chr": "12",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Connective tissue disorder,Stickler syndrome type 1,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.4000000059604645,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1487,
"aa_ref": "G",
"aa_start": 768,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5059,
"cdna_start": 2459,
"cds_end": null,
"cds_length": 4464,
"cds_start": 2304,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "NM_001844.5",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.2304T>C",
"hgvs_p": "p.Gly768Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000380518.8",
"protein_coding": true,
"protein_id": "NP_001835.3",
"strand": false,
"transcript": "NM_001844.5",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1487,
"aa_ref": "G",
"aa_start": 768,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5059,
"cdna_start": 2459,
"cds_end": null,
"cds_length": 4464,
"cds_start": 2304,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000380518.8",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.2304T>C",
"hgvs_p": "p.Gly768Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001844.5",
"protein_coding": true,
"protein_id": "ENSP00000369889.3",
"strand": false,
"transcript": "ENST00000380518.8",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1418,
"aa_ref": "G",
"aa_start": 699,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4442,
"cdna_start": 2282,
"cds_end": null,
"cds_length": 4257,
"cds_start": 2097,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 53,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000337299.7",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.2097T>C",
"hgvs_p": "p.Gly699Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000338213.6",
"strand": false,
"transcript": "ENST00000337299.7",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1488,
"aa_ref": "G",
"aa_start": 769,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5275,
"cdna_start": 2675,
"cds_end": null,
"cds_length": 4467,
"cds_start": 2307,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000928357.1",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.2307T>C",
"hgvs_p": "p.Gly769Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000598416.1",
"strand": false,
"transcript": "ENST00000928357.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1418,
"aa_ref": "G",
"aa_start": 699,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4852,
"cdna_start": 2252,
"cds_end": null,
"cds_length": 4257,
"cds_start": 2097,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 53,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "NM_033150.3",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.2097T>C",
"hgvs_p": "p.Gly699Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_149162.2",
"strand": false,
"transcript": "NM_033150.3",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1535,
"aa_ref": "G",
"aa_start": 816,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5170,
"cdna_start": 2570,
"cds_end": null,
"cds_length": 4608,
"cds_start": 2448,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 56,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "XM_017018828.1",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.2448T>C",
"hgvs_p": "p.Gly816Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016874317.1",
"strand": false,
"transcript": "XM_017018828.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1534,
"aa_ref": "G",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5167,
"cdna_start": 2567,
"cds_end": null,
"cds_length": 4605,
"cds_start": 2445,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 56,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "XM_017018829.1",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.2445T>C",
"hgvs_p": "p.Gly815Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016874318.1",
"strand": false,
"transcript": "XM_017018829.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1465,
"aa_ref": "G",
"aa_start": 746,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4960,
"cdna_start": 2360,
"cds_end": null,
"cds_length": 4398,
"cds_start": 2238,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 55,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "XM_017018830.1",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.2238T>C",
"hgvs_p": "p.Gly746Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016874319.1",
"strand": false,
"transcript": "XM_017018830.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1305,
"aa_ref": "G",
"aa_start": 586,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5388,
"cdna_start": 2788,
"cds_end": null,
"cds_length": 3918,
"cds_start": 1758,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_017018831.3",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.1758T>C",
"hgvs_p": "p.Gly586Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016874320.1",
"strand": false,
"transcript": "XM_017018831.3",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 1305,
"aa_ref": "G",
"aa_start": 586,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4837,
"cdna_start": 2237,
"cds_end": null,
"cds_length": 3918,
"cds_start": 1758,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_047428315.1",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "c.1758T>C",
"hgvs_p": "p.Gly586Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047284271.1",
"strand": false,
"transcript": "XM_047428315.1",
"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": 641,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000483376.1",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "n.482T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000483376.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3756,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 37,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000493991.5",
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"hgvs_c": "n.1228T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000493991.5",
"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": 357,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_944910.2",
"gene_hgnc_id": null,
"gene_symbol": "LOC105369752",
"hgvs_c": "n.219-257A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_944910.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs925297712",
"effect": "splice_region_variant,synonymous_variant",
"frequency_reference_population": 0.0000061976684,
"gene_hgnc_id": 2200,
"gene_symbol": "COL2A1",
"gnomad_exomes_ac": 9,
"gnomad_exomes_af": 0.00000615767,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065825,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Connective tissue disorder|not provided|Stickler syndrome type 1",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.845,
"pos": 47982158,
"ref": "A",
"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_001844.5"
}
]
}