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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: 3-50349690-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=50349690&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 50349690,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000232501.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.314T>C",
"hgvs_p": "p.Leu105Pro",
"transcript": "NM_006545.5",
"protein_id": "NP_006536.3",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 380,
"cds_start": 314,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 437,
"cdna_end": null,
"cdna_length": 1542,
"mane_select": "ENST00000232501.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.314T>C",
"hgvs_p": "p.Leu105Pro",
"transcript": "ENST00000232501.8",
"protein_id": "ENSP00000232501.3",
"transcript_support_level": 1,
"aa_start": 105,
"aa_end": null,
"aa_length": 380,
"cds_start": 314,
"cds_end": null,
"cds_length": 1143,
"cdna_start": 437,
"cdna_end": null,
"cdna_length": 1542,
"mane_select": "NM_006545.5",
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*45T>C",
"hgvs_p": null,
"transcript": "ENST00000451194.5",
"protein_id": "ENSP00000388358.1",
"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": 1747,
"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": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.991T>C",
"hgvs_p": null,
"transcript": "ENST00000461020.5",
"protein_id": null,
"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": 2229,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.996T>C",
"hgvs_p": null,
"transcript": "ENST00000467294.1",
"protein_id": null,
"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": 3113,
"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": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.981T>C",
"hgvs_p": null,
"transcript": "ENST00000487632.5",
"protein_id": null,
"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": 2015,
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*45T>C",
"hgvs_p": null,
"transcript": "ENST00000451194.5",
"protein_id": "ENSP00000388358.1",
"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": 1747,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.171-196T>C",
"hgvs_p": null,
"transcript": "ENST00000429366.5",
"protein_id": "ENSP00000412779.1",
"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": 1364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.392T>C",
"hgvs_p": "p.Leu131Pro",
"transcript": "XM_047447310.1",
"protein_id": "XP_047303266.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 406,
"cds_start": 392,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 690,
"cdna_end": null,
"cdna_length": 1795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.305T>C",
"hgvs_p": "p.Leu102Pro",
"transcript": "XM_011533288.4",
"protein_id": "XP_011531590.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 377,
"cds_start": 305,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 984,
"cdna_end": null,
"cdna_length": 2089,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.392T>C",
"hgvs_p": "p.Leu131Pro",
"transcript": "XM_047447311.1",
"protein_id": "XP_047303267.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 349,
"cds_start": 392,
"cds_end": null,
"cds_length": 1050,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 1317,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.392T>C",
"hgvs_p": "p.Leu131Pro",
"transcript": "XM_047447312.1",
"protein_id": "XP_047303268.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 283,
"cds_start": 392,
"cds_end": null,
"cds_length": 852,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 1095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.314T>C",
"hgvs_p": "p.Leu105Pro",
"transcript": "XM_047447314.1",
"protein_id": "XP_047303270.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 257,
"cds_start": 314,
"cds_end": null,
"cds_length": 774,
"cdna_start": 437,
"cdna_end": null,
"cdna_length": 1049,
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*45T>C",
"hgvs_p": null,
"transcript": "ENST00000418825.5",
"protein_id": "ENSP00000396172.1",
"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": 1030,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*45T>C",
"hgvs_p": null,
"transcript": "ENST00000433381.5",
"protein_id": "ENSP00000388019.1",
"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": 1573,
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*158T>C",
"hgvs_p": null,
"transcript": "ENST00000433999.5",
"protein_id": "ENSP00000415045.1",
"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,
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"cdna_length": 1006,
"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": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*45T>C",
"hgvs_p": null,
"transcript": "ENST00000448302.1",
"protein_id": "ENSP00000389429.1",
"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,
"cdna_end": null,
"cdna_length": 939,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.437T>C",
"hgvs_p": null,
"transcript": "ENST00000469839.1",
"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,
"cdna_end": null,
"cdna_length": 971,
"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": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.538T>C",
"hgvs_p": null,
"transcript": "ENST00000476064.5",
"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": 1643,
"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": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.973T>C",
"hgvs_p": null,
"transcript": "ENST00000479512.5",
"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": 1905,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.676T>C",
"hgvs_p": null,
"transcript": "ENST00000480296.5",
"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,
"cdna_end": null,
"cdna_length": 2512,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.580T>C",
"hgvs_p": null,
"transcript": "ENST00000493907.1",
"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,
"cdna_end": null,
"cdna_length": 835,
"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": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.314T>C",
"hgvs_p": null,
"transcript": "ENST00000667046.1",
"protein_id": "ENSP00000499627.1",
"transcript_support_level": null,
"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": 1371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
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}
],
"gene_symbol": "NPRL2",
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"dbsnp": "rs886037965",
"frequency_reference_population": 6.844543e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84454e-7,
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"gnomad_exomes_ac": 1,
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"gnomad_exomes_homalt": 0,
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"gnomad_mito_homoplasmic": null,
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"computational_score_selected": 0.9444211721420288,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.77,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9991,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.48,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.26,
"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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"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
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"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000232501.8",
"gene_symbol": "NPRL2",
"hgnc_id": 24969,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.314T>C",
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],
"clinvar_disease": " familial focal, with variable foci 2,Epilepsy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Epilepsy, familial focal, with variable foci 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}