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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: 3-120644405-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=120644405&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 120644405,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000187.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Pro230Ser",
"transcript": "NM_000187.4",
"protein_id": "NP_000178.2",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 445,
"cds_start": 688,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000283871.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000187.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Pro230Ser",
"transcript": "ENST00000283871.10",
"protein_id": "ENSP00000283871.5",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 445,
"cds_start": 688,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000187.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000283871.10"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Pro230Ser",
"transcript": "ENST00000898838.1",
"protein_id": "ENSP00000568897.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 499,
"cds_start": 688,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898838.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Pro230Ser",
"transcript": "ENST00000898833.1",
"protein_id": "ENSP00000568892.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 452,
"cds_start": 688,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898833.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Pro228Ser",
"transcript": "ENST00000898830.1",
"protein_id": "ENSP00000568889.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 443,
"cds_start": 682,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898830.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.676C>T",
"hgvs_p": "p.Pro226Ser",
"transcript": "ENST00000898840.1",
"protein_id": "ENSP00000568899.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 441,
"cds_start": 676,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898840.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.616C>T",
"hgvs_p": "p.Pro206Ser",
"transcript": "ENST00000898835.1",
"protein_id": "ENSP00000568894.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 421,
"cds_start": 616,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898835.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Pro204Ser",
"transcript": "ENST00000898841.1",
"protein_id": "ENSP00000568900.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 419,
"cds_start": 610,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898841.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.610C>T",
"hgvs_p": "p.Pro204Ser",
"transcript": "ENST00000955340.1",
"protein_id": "ENSP00000625399.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 419,
"cds_start": 610,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955340.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.421C>T",
"hgvs_p": "p.Pro141Ser",
"transcript": "ENST00000898844.1",
"protein_id": "ENSP00000568903.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 356,
"cds_start": 421,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898844.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Pro230Ser",
"transcript": "ENST00000898832.1",
"protein_id": "ENSP00000568891.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 342,
"cds_start": 688,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898832.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.682C>T",
"hgvs_p": "p.Pro228Ser",
"transcript": "ENST00000898836.1",
"protein_id": "ENSP00000568895.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 340,
"cds_start": 682,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898836.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.106C>T",
"hgvs_p": "p.Pro36Ser",
"transcript": "ENST00000494453.1",
"protein_id": "ENSP00000419163.1",
"transcript_support_level": 3,
"aa_start": 36,
"aa_end": null,
"aa_length": 144,
"cds_start": 106,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000494453.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Pro230Ser",
"transcript": "XM_005247413.3",
"protein_id": "XP_005247470.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 338,
"cds_start": 688,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247413.3"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.265C>T",
"hgvs_p": "p.Pro89Ser",
"transcript": "XM_017006277.3",
"protein_id": "XP_016861766.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 304,
"cds_start": 265,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006277.3"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.Pro230Ser",
"transcript": "XM_011512746.3",
"protein_id": "XP_011511048.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 294,
"cds_start": 688,
"cds_end": null,
"cds_length": 885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512746.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.*162C>T",
"hgvs_p": null,
"transcript": "XM_005247414.6",
"protein_id": "XP_005247471.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 233,
"cds_start": null,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247414.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.549+2568C>T",
"hgvs_p": null,
"transcript": "ENST00000898842.1",
"protein_id": "ENSP00000568901.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 377,
"cds_start": null,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898842.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.549+2568C>T",
"hgvs_p": null,
"transcript": "ENST00000898831.1",
"protein_id": "ENSP00000568890.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 370,
"cds_start": null,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898831.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.543+2568C>T",
"hgvs_p": null,
"transcript": "ENST00000898834.1",
"protein_id": "ENSP00000568893.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 368,
"cds_start": null,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898834.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.649+1862C>T",
"hgvs_p": null,
"transcript": "ENST00000898839.1",
"protein_id": "ENSP00000568898.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 326,
"cds_start": null,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898839.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.549+2568C>T",
"hgvs_p": null,
"transcript": "ENST00000898837.1",
"protein_id": "ENSP00000568896.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 267,
"cds_start": null,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898837.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
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],
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"computational_score_selected": 0.9772851467132568,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.981,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9617,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.356,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_classification": "Pathogenic",
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"acmg_by_gene": [
{
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"pathogenic_score": 19,
"criteria": [
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"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000187.4",
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"effects": [
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],
"clinvar_disease": "Alkaptonuria",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 O:1",
"phenotype_combined": "Alkaptonuria",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}