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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: 3-50350583-TGA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=50350583&ref=TGA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 50350583,
"ref": "TGA",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "NM_006545.5",
"consequences": [
{
"aa_ref": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "NM_006545.5",
"protein_id": "NP_006536.3",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 380,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000232501.8",
"protein_id": "ENSP00000232501.3",
"transcript_support_level": 1,
"aa_start": 23,
"aa_end": null,
"aa_length": 380,
"cds_start": 68,
"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": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.68_69delTC",
"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": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.68_69delTC",
"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": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.198_199delTC",
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.198_199delTC",
"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": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.183_184delTC",
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000894719.1",
"protein_id": "ENSP00000564778.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 392,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000894720.1",
"protein_id": "ENSP00000564779.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 391,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000966296.1",
"protein_id": "ENSP00000636355.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 381,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000894718.1",
"protein_id": "ENSP00000564777.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 370,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000966295.1",
"protein_id": "ENSP00000636354.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 370,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000966297.1",
"protein_id": "ENSP00000636356.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 350,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000931006.1",
"protein_id": "ENSP00000601065.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 323,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "ENST00000931005.1",
"protein_id": "ENSP00000601064.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 298,
"cds_start": 68,
"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": "I",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.68_69delTC",
"hgvs_p": "p.Ile23fs",
"transcript": "XM_047447314.1",
"protein_id": "XP_047303270.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 257,
"cds_start": 68,
"cds_end": null,
"cds_length": 774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447314.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.-108_-107delTC",
"hgvs_p": null,
"transcript": "XM_047447310.1",
"protein_id": "XP_047303266.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 406,
"cds_start": null,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "c.-489_-488delTC",
"hgvs_p": null,
"transcript": "XM_011533288.4",
"protein_id": "XP_011531590.1",
"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": "XM_011533288.4"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.68_69delTC",
"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": 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": "ENST00000418825.5"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.68_69delTC",
"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": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.68_69delTC",
"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": 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": "ENST00000433999.5"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPRL2",
"gene_hgnc_id": 24969,
"hgvs_c": "n.68_69delTC",
"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": 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": "ENST00000448302.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
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],
"gene_symbol": "NPRL2",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
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"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
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"alphamissense_score": null,
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"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.039,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_classification": "Likely_pathogenic",
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"acmg_by_gene": [
{
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"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
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"PM2",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_006545.5",
"gene_symbol": "NPRL2",
"hgnc_id": 24969,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
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"hgvs_p": "p.Ile23fs"
}
],
"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
}