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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: 1-230691475-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=230691475&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COG2",
"hgnc_id": 6546,
"hgvs_c": "c.2026G>A",
"hgvs_p": "p.Ala676Thr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_007357.3",
"verdict": "Benign"
},
{
"benign_score": 9,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "AGT",
"hgnc_id": 333,
"hgvs_c": "c.*2936C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -9,
"transcript": "ENST00000680783.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_score": -9,
"allele_count_reference_population": 733,
"alphamissense_prediction": null,
"alphamissense_score": 0.0647,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.82,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " type IIq,Congenital disorder of glycosylation,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.01204720139503479,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 738,
"aa_ref": "A",
"aa_start": 676,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2932,
"cdna_start": 2152,
"cds_end": null,
"cds_length": 2217,
"cds_start": 2026,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_007357.3",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.2026G>A",
"hgvs_p": "p.Ala676Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000366669.9",
"protein_coding": true,
"protein_id": "NP_031383.1",
"strand": true,
"transcript": "NM_007357.3",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 738,
"aa_ref": "A",
"aa_start": 676,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2932,
"cdna_start": 2152,
"cds_end": null,
"cds_length": 2217,
"cds_start": 2026,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000366669.9",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.2026G>A",
"hgvs_p": "p.Ala676Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007357.3",
"protein_coding": true,
"protein_id": "ENSP00000355629.4",
"strand": true,
"transcript": "ENST00000366669.9",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 737,
"aa_ref": "A",
"aa_start": 675,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2843,
"cdna_start": 2063,
"cds_end": null,
"cds_length": 2214,
"cds_start": 2023,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000366668.7",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.2023G>A",
"hgvs_p": "p.Ala675Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000355628.3",
"strand": true,
"transcript": "ENST00000366668.7",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 737,
"aa_ref": "A",
"aa_start": 675,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2929,
"cdna_start": 2149,
"cds_end": null,
"cds_length": 2214,
"cds_start": 2023,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001145036.2",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.2023G>A",
"hgvs_p": "p.Ala675Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001138508.1",
"strand": true,
"transcript": "NM_001145036.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 737,
"aa_ref": "A",
"aa_start": 675,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2930,
"cdna_start": 2149,
"cds_end": null,
"cds_length": 2214,
"cds_start": 2023,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000921491.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.2023G>A",
"hgvs_p": "p.Ala675Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591550.1",
"strand": true,
"transcript": "ENST00000921491.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 731,
"aa_ref": "A",
"aa_start": 676,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2928,
"cdna_start": 2169,
"cds_end": null,
"cds_length": 2196,
"cds_start": 2026,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000964684.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.2026G>A",
"hgvs_p": "p.Ala676Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634743.1",
"strand": true,
"transcript": "ENST00000964684.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 716,
"aa_ref": "A",
"aa_start": 654,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2865,
"cdna_start": 2086,
"cds_end": null,
"cds_length": 2151,
"cds_start": 1960,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000964685.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1960G>A",
"hgvs_p": "p.Ala654Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634744.1",
"strand": true,
"transcript": "ENST00000964685.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 679,
"aa_ref": "A",
"aa_start": 617,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2963,
"cdna_start": 2184,
"cds_end": null,
"cds_length": 2040,
"cds_start": 1849,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000534989.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1849G>A",
"hgvs_p": "p.Ala617Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000440349.1",
"strand": true,
"transcript": "ENST00000534989.1",
"transcript_support_level": 2
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 678,
"aa_ref": "A",
"aa_start": 616,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2750,
"cdna_start": 1967,
"cds_end": null,
"cds_length": 2037,
"cds_start": 1846,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000865123.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1846G>A",
"hgvs_p": "p.Ala616Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535182.1",
"strand": true,
"transcript": "ENST00000865123.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 677,
"aa_ref": "A",
"aa_start": 615,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2724,
"cdna_start": 1945,
"cds_end": null,
"cds_length": 2034,
"cds_start": 1843,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000865124.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1843G>A",
"hgvs_p": "p.Ala615Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535183.1",
"strand": true,
"transcript": "ENST00000865124.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 675,
"aa_ref": "A",
"aa_start": 613,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2736,
"cdna_start": 1957,
"cds_end": null,
"cds_length": 2028,
"cds_start": 1837,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000964686.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1837G>A",
"hgvs_p": "p.Ala613Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634745.1",
"strand": true,
"transcript": "ENST00000964686.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 662,
"aa_ref": "A",
"aa_start": 600,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2696,
"cdna_start": 1919,
"cds_end": null,
"cds_length": 1989,
"cds_start": 1798,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000964687.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1798G>A",
"hgvs_p": "p.Ala600Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634746.1",
"strand": true,
"transcript": "ENST00000964687.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 600,
"aa_ref": "A",
"aa_start": 538,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2486,
"cdna_start": 1708,
"cds_end": null,
"cds_length": 1803,
"cds_start": 1612,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000964688.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1612G>A",
"hgvs_p": "p.Ala538Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634747.1",
"strand": true,
"transcript": "ENST00000964688.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 420,
"aa_ref": "A",
"aa_start": 358,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1727,
"cdna_start": 1198,
"cds_end": null,
"cds_length": 1263,
"cds_start": 1072,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000964689.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1072G>A",
"hgvs_p": "p.Ala358Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000634748.1",
"strand": true,
"transcript": "ENST00000964689.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 625,
"aa_ref": "A",
"aa_start": 563,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2573,
"cdna_start": 1793,
"cds_end": null,
"cds_length": 1878,
"cds_start": 1687,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_047449445.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "c.1687G>A",
"hgvs_p": "p.Ala563Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047305401.1",
"strand": true,
"transcript": "XM_047449445.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5004,
"cdna_start": null,
"cds_end": null,
"cds_length": 858,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000680783.1",
"gene_hgnc_id": 333,
"gene_symbol": "AGT",
"hgvs_c": "c.*2936C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000506329.1",
"strand": false,
"transcript": "ENST00000680783.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2784,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000468893.6",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "n.*1884G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000476305.1",
"strand": true,
"transcript": "ENST00000468893.6",
"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": 629,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000478710.1",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "n.285G>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": "ENST00000478710.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2784,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000468893.6",
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"hgvs_c": "n.*1884G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000476305.1",
"strand": true,
"transcript": "ENST00000468893.6",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs149248784",
"effect": "missense_variant",
"frequency_reference_population": 0.00045416242,
"gene_hgnc_id": 6546,
"gene_symbol": "COG2",
"gnomad_exomes_ac": 688,
"gnomad_exomes_af": 0.000470638,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 45,
"gnomad_genomes_af": 0.000295827,
"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": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Congenital disorder of glycosylation, type IIq|not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -2.893,
"pos": 230691475,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.018,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
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"transcript": "NM_007357.3"
}
]
}