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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: 5-96393270-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=96393270&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 96393270,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000311106.8",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK1",
"gene_hgnc_id": 8743,
"hgvs_c": "c.1993C>G",
"hgvs_p": "p.Gln665Glu",
"transcript": "NM_000439.5",
"protein_id": "NP_000430.3",
"transcript_support_level": null,
"aa_start": 665,
"aa_end": null,
"aa_length": 753,
"cds_start": 1993,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2199,
"cdna_end": null,
"cdna_length": 5136,
"mane_select": "ENST00000311106.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK1",
"gene_hgnc_id": 8743,
"hgvs_c": "c.1993C>G",
"hgvs_p": "p.Gln665Glu",
"transcript": "ENST00000311106.8",
"protein_id": "ENSP00000308024.2",
"transcript_support_level": 1,
"aa_start": 665,
"aa_end": null,
"aa_length": 753,
"cds_start": 1993,
"cds_end": null,
"cds_length": 2262,
"cdna_start": 2199,
"cdna_end": null,
"cdna_length": 5136,
"mane_select": "NM_000439.5",
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK1",
"gene_hgnc_id": 8743,
"hgvs_c": "n.1136C>G",
"hgvs_p": null,
"transcript": "ENST00000513085.1",
"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": 1481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK1",
"gene_hgnc_id": 8743,
"hgvs_c": "c.1852C>G",
"hgvs_p": "p.Gln618Glu",
"transcript": "NM_001177875.2",
"protein_id": "NP_001171346.1",
"transcript_support_level": null,
"aa_start": 618,
"aa_end": null,
"aa_length": 706,
"cds_start": 1852,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 1891,
"cdna_end": null,
"cdna_length": 4828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK1",
"gene_hgnc_id": 8743,
"hgvs_c": "c.1852C>G",
"hgvs_p": "p.Gln618Glu",
"transcript": "ENST00000508626.5",
"protein_id": "ENSP00000421600.1",
"transcript_support_level": 2,
"aa_start": 618,
"aa_end": null,
"aa_length": 706,
"cds_start": 1852,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 1891,
"cdna_end": null,
"cdna_length": 2234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423250.1",
"protein_id": "NP_001410179.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 708,
"cds_start": -4,
"cds_end": null,
"cds_length": 2127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423251.1",
"protein_id": "NP_001410180.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 695,
"cds_start": -4,
"cds_end": null,
"cds_length": 2088,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423252.1",
"protein_id": "NP_001410181.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 695,
"cds_start": -4,
"cds_end": null,
"cds_length": 2088,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4639,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-103+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423253.1",
"protein_id": "NP_001410182.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 686,
"cds_start": -4,
"cds_end": null,
"cds_length": 2061,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423254.1",
"protein_id": "NP_001410183.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 686,
"cds_start": -4,
"cds_end": null,
"cds_length": 2061,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4619,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423255.1",
"protein_id": "NP_001410184.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 673,
"cds_start": -4,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423256.1",
"protein_id": "NP_001410185.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 673,
"cds_start": -4,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423257.1",
"protein_id": "NP_001410186.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 673,
"cds_start": -4,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
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"cdna_length": 4573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-40+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423258.1",
"protein_id": "NP_001410187.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 673,
"cds_start": -4,
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"cds_length": 2022,
"cdna_start": null,
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"cdna_length": 4490,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 32,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423259.1",
"protein_id": "NP_001410188.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 672,
"cds_start": -4,
"cds_end": null,
"cds_length": 2019,
"cdna_start": null,
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"cdna_length": 4577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "NM_001423260.1",
"protein_id": "NP_001410189.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"biotype": null,
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},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 31,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": null,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "ENST00000718093.1",
"protein_id": "ENSP00000520668.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 654,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 4167,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": null,
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null,
"transcript": "ENST00000718091.1",
"protein_id": "ENSP00000520667.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 142,
"cds_start": -4,
"cds_end": null,
"cds_length": 429,
"cdna_start": null,
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"cdna_length": 1835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "n.449+13618G>C",
"hgvs_p": null,
"transcript": "ENST00000718089.1",
"protein_id": null,
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"aa_start": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CAST",
"gene_hgnc_id": 1515,
"hgvs_c": "n.240+13618G>C",
"hgvs_p": null,
"transcript": "ENST00000718090.1",
"protein_id": null,
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"cdna_length": 359,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "LOC101929710",
"gene_hgnc_id": null,
"hgvs_c": "n.354+13618G>C",
"hgvs_p": null,
"transcript": "NR_130776.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PCSK1",
"gene_hgnc_id": 8743,
"dbsnp": "rs6234",
"frequency_reference_population": 0.2653991,
"hom_count_reference_population": 57709,
"allele_count_reference_population": 428257,
"gnomad_exomes_af": 0.267766,
"gnomad_genomes_af": 0.242643,
"gnomad_exomes_ac": 391365,
"gnomad_genomes_ac": 36892,
"gnomad_exomes_homalt": 53056,
"gnomad_genomes_homalt": 4653,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003394097089767456,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.081,
"revel_prediction": "Benign",
"alphamissense_score": 0.0507,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.11,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000311106.8",
"gene_symbol": "PCSK1",
"hgnc_id": 8743,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1993C>G",
"hgvs_p": "p.Gln665Glu"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001423250.1",
"gene_symbol": "CAST",
"hgnc_id": 1515,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-175+13618G>C",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NR_130776.1",
"gene_symbol": "LOC101929710",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.354+13618G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Monogenic Non-Syndromic Obesity,Obesity due to prohormone convertase I deficiency,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:3",
"phenotype_combined": "Obesity due to prohormone convertase I deficiency|Monogenic Non-Syndromic Obesity|not provided|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}