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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: 2-219557459-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=219557459&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 219557459,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000404537.6",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "NM_015311.3",
"protein_id": "NP_056126.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1896,
"cds_start": 3950,
"cds_end": null,
"cds_length": 5691,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 6105,
"mane_select": "ENST00000404537.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "ENST00000404537.6",
"protein_id": "ENSP00000385636.1",
"transcript_support_level": 1,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1896,
"cds_start": 3950,
"cds_end": null,
"cds_length": 5691,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 6105,
"mane_select": "NM_015311.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "NM_001173431.2",
"protein_id": "NP_001166902.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1543,
"cds_start": 3950,
"cds_end": null,
"cds_length": 4632,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 5787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "ENST00000603926.5",
"protein_id": "ENSP00000474519.1",
"transcript_support_level": 5,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1543,
"cds_start": 3950,
"cds_end": null,
"cds_length": 4632,
"cdna_start": 4007,
"cdna_end": null,
"cdna_length": 5520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "XM_011510857.3",
"protein_id": "XP_011509159.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1918,
"cds_start": 3950,
"cds_end": null,
"cds_length": 5757,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 8306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "XM_017003696.3",
"protein_id": "XP_016859185.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1908,
"cds_start": 3950,
"cds_end": null,
"cds_length": 5727,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 6548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "XM_017003697.3",
"protein_id": "XP_016859186.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1908,
"cds_start": 3950,
"cds_end": null,
"cds_length": 5727,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 6131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3674T>A",
"hgvs_p": "p.Leu1225Gln",
"transcript": "XM_017003699.2",
"protein_id": "XP_016859188.1",
"transcript_support_level": null,
"aa_start": 1225,
"aa_end": null,
"aa_length": 1826,
"cds_start": 3674,
"cds_end": null,
"cds_length": 5481,
"cdna_start": 3981,
"cdna_end": null,
"cdna_length": 8030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "XM_011510863.4",
"protein_id": "XP_011509165.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1543,
"cds_start": 3950,
"cds_end": null,
"cds_length": 4632,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 4954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "XM_011510864.3",
"protein_id": "XP_011509166.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1493,
"cds_start": 3950,
"cds_end": null,
"cds_length": 4482,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 5663,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln",
"transcript": "XM_011510865.3",
"protein_id": "XP_011509167.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1493,
"cds_start": 3950,
"cds_end": null,
"cds_length": 4482,
"cdna_start": 4257,
"cdna_end": null,
"cdna_length": 4901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3674T>A",
"hgvs_p": "p.Leu1225Gln",
"transcript": "XM_011510866.3",
"protein_id": "XP_011509168.1",
"transcript_support_level": null,
"aa_start": 1225,
"aa_end": null,
"aa_length": 1401,
"cds_start": 3674,
"cds_end": null,
"cds_length": 4206,
"cdna_start": 3981,
"cdna_end": null,
"cdna_length": 5387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "n.3181T>A",
"hgvs_p": null,
"transcript": "ENST00000465149.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 5380,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3790+364T>A",
"hgvs_p": null,
"transcript": "ENST00000373876.5",
"protein_id": "ENSP00000362983.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1804,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"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": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.769+364T>A",
"hgvs_p": null,
"transcript": "ENST00000456147.1",
"protein_id": "ENSP00000403665.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 444,
"cds_start": -4,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
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"cdna_length": 1571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"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": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.670+364T>A",
"hgvs_p": null,
"transcript": "ENST00000604031.5",
"protein_id": "ENSP00000475126.1",
"transcript_support_level": 2,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000269068",
"gene_hgnc_id": null,
"hgvs_c": "n.714+724A>T",
"hgvs_p": null,
"transcript": "ENST00000793735.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1129,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3790+364T>A",
"hgvs_p": null,
"transcript": "XM_017003698.2",
"protein_id": "XP_016859187.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1826,
"cds_start": -4,
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"cdna_start": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3514+364T>A",
"hgvs_p": null,
"transcript": "XM_017003700.2",
"protein_id": "XP_016859189.1",
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3790+364T>A",
"hgvs_p": null,
"transcript": "XM_047443799.1",
"protein_id": "XP_047299755.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 12,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"hgvs_c": "c.3514+364T>A",
"hgvs_p": null,
"transcript": "XM_047443800.1",
"protein_id": "XP_047299756.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1309,
"cds_start": -4,
"cds_end": null,
"cds_length": 3930,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OBSL1",
"gene_hgnc_id": 29092,
"dbsnp": "rs115283876",
"frequency_reference_population": 0.0015238961,
"hom_count_reference_population": 34,
"allele_count_reference_population": 2360,
"gnomad_exomes_af": 0.000850061,
"gnomad_genomes_af": 0.00770231,
"gnomad_exomes_ac": 1187,
"gnomad_genomes_ac": 1173,
"gnomad_exomes_homalt": 19,
"gnomad_genomes_homalt": 15,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008046150207519531,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.483,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1504,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.545,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000404537.6",
"gene_symbol": "OBSL1",
"hgnc_id": 29092,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3950T>A",
"hgvs_p": "p.Leu1317Gln"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000793735.1",
"gene_symbol": "ENSG00000269068",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.714+724A>T",
"hgvs_p": null
}
],
"clinvar_disease": "3M syndrome 2,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "3M syndrome 2|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}