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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: 3-50347777-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=50347777&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 50347777,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006545.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1057G>A",
"hgvs_p": "p.Glu353Lys",
"transcript": "NM_006545.5",
"protein_id": "NP_006536.3",
"transcript_support_level": null,
"aa_start": 353,
"aa_end": null,
"aa_length": 380,
"cds_start": 1057,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000232501.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006545.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1057G>A",
"hgvs_p": "p.Glu353Lys",
"transcript": "ENST00000232501.8",
"protein_id": "ENSP00000232501.3",
"transcript_support_level": 1,
"aa_start": 353,
"aa_end": null,
"aa_length": 380,
"cds_start": 1057,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006545.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000232501.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*936G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000429366.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*1180G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000451194.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.2025G>A",
"hgvs_p": null,
"transcript": "ENST00000461020.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000461020.5"
},
{
"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.2909G>A",
"hgvs_p": null,
"transcript": "ENST00000467294.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000467294.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.1811G>A",
"hgvs_p": null,
"transcript": "ENST00000487632.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000487632.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*936G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000429366.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*1180G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000451194.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1093G>A",
"hgvs_p": "p.Glu365Lys",
"transcript": "ENST00000894719.1",
"protein_id": "ENSP00000564778.1",
"transcript_support_level": null,
"aa_start": 365,
"aa_end": null,
"aa_length": 392,
"cds_start": 1093,
"cds_end": null,
"cds_length": 1179,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894719.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1090G>A",
"hgvs_p": "p.Glu364Lys",
"transcript": "ENST00000894720.1",
"protein_id": "ENSP00000564779.1",
"transcript_support_level": null,
"aa_start": 364,
"aa_end": null,
"aa_length": 391,
"cds_start": 1090,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894720.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1060G>A",
"hgvs_p": "p.Glu354Lys",
"transcript": "ENST00000966296.1",
"protein_id": "ENSP00000636355.1",
"transcript_support_level": null,
"aa_start": 354,
"aa_end": null,
"aa_length": 381,
"cds_start": 1060,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966296.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1027G>A",
"hgvs_p": "p.Glu343Lys",
"transcript": "ENST00000894718.1",
"protein_id": "ENSP00000564777.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 370,
"cds_start": 1027,
"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": "ENST00000894718.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1027G>A",
"hgvs_p": "p.Glu343Lys",
"transcript": "ENST00000966295.1",
"protein_id": "ENSP00000636354.1",
"transcript_support_level": null,
"aa_start": 343,
"aa_end": null,
"aa_length": 370,
"cds_start": 1027,
"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": "ENST00000966295.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.967G>A",
"hgvs_p": "p.Glu323Lys",
"transcript": "ENST00000966297.1",
"protein_id": "ENSP00000636356.1",
"transcript_support_level": null,
"aa_start": 323,
"aa_end": null,
"aa_length": 350,
"cds_start": 967,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966297.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.886G>A",
"hgvs_p": "p.Glu296Lys",
"transcript": "ENST00000931006.1",
"protein_id": "ENSP00000601065.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 323,
"cds_start": 886,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931006.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.811G>A",
"hgvs_p": "p.Glu271Lys",
"transcript": "ENST00000931005.1",
"protein_id": "ENSP00000601064.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 298,
"cds_start": 811,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931005.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1135G>A",
"hgvs_p": "p.Glu379Lys",
"transcript": "XM_047447310.1",
"protein_id": "XP_047303266.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 406,
"cds_start": 1135,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447310.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Glu350Lys",
"transcript": "XM_011533288.4",
"protein_id": "XP_011531590.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 377,
"cds_start": 1048,
"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": "XM_011533288.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.697G>A",
"hgvs_p": "p.Glu233Lys",
"transcript": "XM_017005556.3",
"protein_id": "XP_016861045.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 260,
"cds_start": 697,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005556.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.*1006G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000433381.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.1281G>A",
"hgvs_p": null,
"transcript": "ENST00000476064.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000476064.5"
},
{
"aa_ref": null,
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{
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],
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],
"gene_symbol": "NPRL2",
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"dbsnp": "rs764349526",
"frequency_reference_population": 0.0000061964547,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000273664,
"gnomad_genomes_af": 0.000039427,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7582964301109314,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.377,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8265,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.943,
"phylop100way_prediction": "Uncertain_significance",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_006545.5",
"gene_symbol": "NPRL2",
"hgnc_id": 24969,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1057G>A",
"hgvs_p": "p.Glu353Lys"
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],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}