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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: 2-165154502-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165154502&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165154502,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_006922.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "NM_006922.4",
"protein_id": "NP_008853.3",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 2000,
"cds_start": 1330,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 9102,
"mane_select": "ENST00000283254.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "ENST00000283254.12",
"protein_id": "ENSP00000283254.7",
"transcript_support_level": 1,
"aa_start": 444,
"aa_end": null,
"aa_length": 2000,
"cds_start": 1330,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 9102,
"mane_select": "NM_006922.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "ENST00000409101.7",
"protein_id": "ENSP00000386726.3",
"transcript_support_level": 1,
"aa_start": 444,
"aa_end": null,
"aa_length": 1951,
"cds_start": 1330,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 1641,
"cdna_end": null,
"cdna_length": 6599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "ENST00000706067.1",
"protein_id": "ENSP00000516211.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1983,
"cds_start": 1330,
"cds_end": null,
"cds_length": 5952,
"cdna_start": 1639,
"cdna_end": null,
"cdna_length": 8869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "ENST00000639244.1",
"protein_id": "ENSP00000492251.1",
"transcript_support_level": 5,
"aa_start": 444,
"aa_end": null,
"aa_length": 1979,
"cds_start": 1330,
"cds_end": null,
"cds_length": 5940,
"cdna_start": 1636,
"cdna_end": null,
"cdna_length": 8854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "NM_001081676.2",
"protein_id": "NP_001075145.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1951,
"cds_start": 1330,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 8955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "NM_001081677.2",
"protein_id": "NP_001075146.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1951,
"cds_start": 1330,
"cds_end": null,
"cds_length": 5856,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 8955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "ENST00000440431.6",
"protein_id": "ENSP00000403348.1",
"transcript_support_level": 5,
"aa_start": 444,
"aa_end": null,
"aa_length": 1363,
"cds_start": 1330,
"cds_end": null,
"cds_length": 4092,
"cdna_start": 1384,
"cdna_end": null,
"cdna_length": 4146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "ENST00000668657.1",
"protein_id": "ENSP00000499420.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1086,
"cds_start": 1330,
"cds_end": null,
"cds_length": 3261,
"cdna_start": 1646,
"cdna_end": null,
"cdna_length": 5424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_011511610.4",
"protein_id": "XP_011509912.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 2000,
"cds_start": 1330,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 1945,
"cdna_end": null,
"cdna_length": 9242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_017004660.3",
"protein_id": "XP_016860149.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 2000,
"cds_start": 1330,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 9102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_017004661.3",
"protein_id": "XP_016860150.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1983,
"cds_start": 1330,
"cds_end": null,
"cds_length": 5952,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 9051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_047445394.1",
"protein_id": "XP_047301350.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1983,
"cds_start": 1330,
"cds_end": null,
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"cdna_start": 1805,
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"cdna_length": 9051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_017004662.3",
"protein_id": "XP_016860151.1",
"transcript_support_level": null,
"aa_start": 444,
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"cds_start": 1330,
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"cdna_start": 1805,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_047445395.1",
"protein_id": "XP_047301351.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1257,
"cds_start": 1330,
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"cdna_start": 1805,
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"cdna_length": 4387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_017004664.2",
"protein_id": "XP_016860153.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_017004665.2",
"protein_id": "XP_016860154.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1086,
"cds_start": 1330,
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"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 11047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*",
"transcript": "XM_017004666.2",
"protein_id": "XP_016860155.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 1083,
"cds_start": 1330,
"cds_end": null,
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"cdna_start": 1805,
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"cdna_length": 11038,
"mane_select": null,
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"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": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "n.1330G>T",
"hgvs_p": null,
"transcript": "ENST00000638473.1",
"protein_id": "ENSP00000491552.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"hgvs_c": "n.1330G>T",
"hgvs_p": null,
"transcript": "ENST00000640652.1",
"protein_id": "ENSP00000492807.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236283",
"gene_hgnc_id": null,
"hgvs_c": "n.320+24298C>A",
"hgvs_p": null,
"transcript": "ENST00000625505.2",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ENSG00000236283",
"gene_hgnc_id": null,
"hgvs_c": "n.643+14793C>A",
"hgvs_p": null,
"transcript": "ENST00000629817.2",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN3A",
"gene_hgnc_id": 10590,
"dbsnp": "rs771117930",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6600000262260437,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"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": 0.66,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "NM_006922.4",
"gene_symbol": "SCN3A",
"hgnc_id": 10590,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1330G>T",
"hgvs_p": "p.Glu444*"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000625505.2",
"gene_symbol": "ENSG00000236283",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.320+24298C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}