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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: 2-25234340-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=25234340&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 25234340,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_022552.5",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2678G>A",
"hgvs_p": "p.Trp893*",
"transcript": "NM_022552.5",
"protein_id": "NP_072046.2",
"transcript_support_level": null,
"aa_start": 893,
"aa_end": null,
"aa_length": 912,
"cds_start": 2678,
"cds_end": null,
"cds_length": 2739,
"cdna_start": 2955,
"cdna_end": null,
"cdna_length": 9421,
"mane_select": "ENST00000321117.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2678G>A",
"hgvs_p": "p.Trp893*",
"transcript": "ENST00000321117.10",
"protein_id": "ENSP00000324375.5",
"transcript_support_level": 1,
"aa_start": 893,
"aa_end": null,
"aa_length": 912,
"cds_start": 2678,
"cds_end": null,
"cds_length": 2739,
"cdna_start": 2955,
"cdna_end": null,
"cdna_length": 9421,
"mane_select": "NM_022552.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2678G>A",
"hgvs_p": "p.Trp893*",
"transcript": "ENST00000264709.7",
"protein_id": "ENSP00000264709.3",
"transcript_support_level": 1,
"aa_start": 893,
"aa_end": null,
"aa_length": 912,
"cds_start": 2678,
"cds_end": null,
"cds_length": 2739,
"cdna_start": 3016,
"cdna_end": null,
"cdna_length": 9501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2111G>A",
"hgvs_p": "p.Trp704*",
"transcript": "ENST00000380746.8",
"protein_id": "ENSP00000370122.4",
"transcript_support_level": 1,
"aa_start": 704,
"aa_end": null,
"aa_length": 723,
"cds_start": 2111,
"cds_end": null,
"cds_length": 2172,
"cdna_start": 2225,
"cdna_end": null,
"cdna_length": 3589,
"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": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "n.*531G>A",
"hgvs_p": null,
"transcript": "ENST00000380756.7",
"protein_id": "ENSP00000370132.3",
"transcript_support_level": 1,
"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": 4477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "n.*531G>A",
"hgvs_p": null,
"transcript": "ENST00000380756.7",
"protein_id": "ENSP00000370132.3",
"transcript_support_level": 1,
"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": 4477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2678G>A",
"hgvs_p": "p.Trp893*",
"transcript": "NM_175629.2",
"protein_id": "NP_783328.1",
"transcript_support_level": null,
"aa_start": 893,
"aa_end": null,
"aa_length": 912,
"cds_start": 2678,
"cds_end": null,
"cds_length": 2739,
"cdna_start": 3016,
"cdna_end": null,
"cdna_length": 4395,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2222G>A",
"hgvs_p": "p.Trp741*",
"transcript": "NM_001320893.1",
"protein_id": "NP_001307822.1",
"transcript_support_level": null,
"aa_start": 741,
"aa_end": null,
"aa_length": 760,
"cds_start": 2222,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 2259,
"cdna_end": null,
"cdna_length": 3638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2111G>A",
"hgvs_p": "p.Trp704*",
"transcript": "NM_153759.3",
"protein_id": "NP_715640.2",
"transcript_support_level": null,
"aa_start": 704,
"aa_end": null,
"aa_length": 723,
"cds_start": 2111,
"cds_end": null,
"cds_length": 2172,
"cdna_start": 2229,
"cdna_end": null,
"cdna_length": 3608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2009G>A",
"hgvs_p": "p.Trp670*",
"transcript": "NM_001375819.1",
"protein_id": "NP_001362748.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 689,
"cds_start": 2009,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2109,
"cdna_end": null,
"cdna_length": 3473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2009G>A",
"hgvs_p": "p.Trp670*",
"transcript": "ENST00000402667.1",
"protein_id": "ENSP00000384237.1",
"transcript_support_level": 5,
"aa_start": 670,
"aa_end": null,
"aa_length": 689,
"cds_start": 2009,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2157,
"cdna_end": null,
"cdna_length": 2300,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2009G>A",
"hgvs_p": "p.Trp670*",
"transcript": "ENST00000683760.1",
"protein_id": "ENSP00000507765.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 689,
"cds_start": 2009,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2260,
"cdna_end": null,
"cdna_length": 3585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2678G>A",
"hgvs_p": "p.Trp893*",
"transcript": "XM_005264175.6",
"protein_id": "XP_005264232.1",
"transcript_support_level": null,
"aa_start": 893,
"aa_end": null,
"aa_length": 912,
"cds_start": 2678,
"cds_end": null,
"cds_length": 2739,
"cdna_start": 5213,
"cdna_end": null,
"cdna_length": 11679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2678G>A",
"hgvs_p": "p.Trp893*",
"transcript": "XM_017003526.2",
"protein_id": "XP_016859015.1",
"transcript_support_level": null,
"aa_start": 893,
"aa_end": null,
"aa_length": 912,
"cds_start": 2678,
"cds_end": null,
"cds_length": 2739,
"cdna_start": 3005,
"cdna_end": null,
"cdna_length": 9471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2531G>A",
"hgvs_p": "p.Trp844*",
"transcript": "XM_011532662.3",
"protein_id": "XP_011530964.1",
"transcript_support_level": null,
"aa_start": 844,
"aa_end": null,
"aa_length": 863,
"cds_start": 2531,
"cds_end": null,
"cds_length": 2592,
"cdna_start": 3783,
"cdna_end": null,
"cdna_length": 10249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2381G>A",
"hgvs_p": "p.Trp794*",
"transcript": "XM_047443592.1",
"protein_id": "XP_047299548.1",
"transcript_support_level": null,
"aa_start": 794,
"aa_end": null,
"aa_length": 813,
"cds_start": 2381,
"cds_end": null,
"cds_length": 2442,
"cdna_start": 2481,
"cdna_end": null,
"cdna_length": 8947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2198G>A",
"hgvs_p": "p.Trp733*",
"transcript": "XM_047443594.1",
"protein_id": "XP_047299550.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 752,
"cds_start": 2198,
"cds_end": null,
"cds_length": 2259,
"cdna_start": 2505,
"cdna_end": null,
"cdna_length": 8971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2150G>A",
"hgvs_p": "p.Trp717*",
"transcript": "XM_011532666.3",
"protein_id": "XP_011530968.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 736,
"cds_start": 2150,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 2268,
"cdna_end": null,
"cdna_length": 8734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2009G>A",
"hgvs_p": "p.Trp670*",
"transcript": "XM_011532667.4",
"protein_id": "XP_011530969.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 689,
"cds_start": 2009,
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"cdna_start": 2101,
"cdna_end": null,
"cdna_length": 8567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2009G>A",
"hgvs_p": "p.Trp670*",
"transcript": "XM_017003527.2",
"protein_id": "XP_016859016.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 689,
"cds_start": 2009,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2209,
"cdna_end": null,
"cdna_length": 8675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2009G>A",
"hgvs_p": "p.Trp670*",
"transcript": "XM_047443596.1",
"protein_id": "XP_047299552.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 689,
"cds_start": 2009,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2327,
"cdna_end": null,
"cdna_length": 8793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
"gene_hgnc_id": 2978,
"hgvs_c": "c.2009G>A",
"hgvs_p": "p.Trp670*",
"transcript": "XM_047443597.1",
"protein_id": "XP_047299553.1",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 689,
"cds_start": 2009,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2366,
"cdna_end": null,
"cdna_length": 8832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNMT3A",
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"hgvs_c": "c.2009G>A",
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{
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{
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}
],
"gene_symbol": "DNMT3A",
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"dbsnp": "rs750515748",
"frequency_reference_population": 0.0000018586969,
"hom_count_reference_population": 0,
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"gnomad_exomes_af": 0.00000136817,
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"gnomad_exomes_ac": 2,
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"computational_score_selected": 0.6499999761581421,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.65,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.902,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
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"apogee2_score": null,
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"mitotip_score": null,
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"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
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"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_022552.5",
"gene_symbol": "DNMT3A",
"hgnc_id": 2978,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD",
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],
"clinvar_disease": "Tatton-Brown-Rahman overgrowth syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Tatton-Brown-Rahman overgrowth syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}