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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: 1-55061540-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=55061540&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 55061540,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000302118.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1847C>T",
"hgvs_p": "p.Pro616Leu",
"transcript": "NM_174936.4",
"protein_id": "NP_777596.2",
"transcript_support_level": null,
"aa_start": 616,
"aa_end": null,
"aa_length": 692,
"cds_start": 1847,
"cds_end": null,
"cds_length": 2079,
"cdna_start": 2137,
"cdna_end": null,
"cdna_length": 3637,
"mane_select": "ENST00000302118.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1847C>T",
"hgvs_p": "p.Pro616Leu",
"transcript": "ENST00000302118.5",
"protein_id": "ENSP00000303208.5",
"transcript_support_level": 1,
"aa_start": 616,
"aa_end": null,
"aa_length": 692,
"cds_start": 1847,
"cds_end": null,
"cds_length": 2079,
"cdna_start": 2137,
"cdna_end": null,
"cdna_length": 3637,
"mane_select": "NM_174936.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.2204C>T",
"hgvs_p": "p.Pro735Leu",
"transcript": "ENST00000710286.1",
"protein_id": "ENSP00000518176.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 811,
"cds_start": 2204,
"cds_end": null,
"cds_length": 2436,
"cdna_start": 2229,
"cdna_end": null,
"cdna_length": 3729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1970C>T",
"hgvs_p": "p.Pro657Leu",
"transcript": "NM_001407240.1",
"protein_id": "NP_001394169.1",
"transcript_support_level": null,
"aa_start": 657,
"aa_end": null,
"aa_length": 733,
"cds_start": 1970,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2260,
"cdna_end": null,
"cdna_length": 3760,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1970C>T",
"hgvs_p": "p.Pro657Leu",
"transcript": "ENST00000713786.1",
"protein_id": "ENSP00000519088.1",
"transcript_support_level": null,
"aa_start": 657,
"aa_end": null,
"aa_length": 733,
"cds_start": 1970,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2340,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1889C>T",
"hgvs_p": "p.Pro630Leu",
"transcript": "NM_001407241.1",
"protein_id": "NP_001394170.1",
"transcript_support_level": null,
"aa_start": 630,
"aa_end": null,
"aa_length": 706,
"cds_start": 1889,
"cds_end": null,
"cds_length": 2121,
"cdna_start": 2179,
"cdna_end": null,
"cdna_length": 3679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1850C>T",
"hgvs_p": "p.Pro617Leu",
"transcript": "NM_001407242.1",
"protein_id": "NP_001394171.1",
"transcript_support_level": null,
"aa_start": 617,
"aa_end": null,
"aa_length": 693,
"cds_start": 1850,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 2140,
"cdna_end": null,
"cdna_length": 3640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1790C>T",
"hgvs_p": "p.Pro597Leu",
"transcript": "NM_001407243.1",
"protein_id": "NP_001394172.1",
"transcript_support_level": null,
"aa_start": 597,
"aa_end": null,
"aa_length": 673,
"cds_start": 1790,
"cds_end": null,
"cds_length": 2022,
"cdna_start": 2080,
"cdna_end": null,
"cdna_length": 3580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1673C>T",
"hgvs_p": "p.Pro558Leu",
"transcript": "NM_001407244.1",
"protein_id": "NP_001394173.1",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 634,
"cds_start": 1673,
"cds_end": null,
"cds_length": 1905,
"cdna_start": 1963,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1655C>T",
"hgvs_p": "p.Pro552Leu",
"transcript": "NM_001407245.1",
"protein_id": "NP_001394174.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 628,
"cds_start": 1655,
"cds_end": null,
"cds_length": 1887,
"cdna_start": 1945,
"cdna_end": null,
"cdna_length": 3445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1472C>T",
"hgvs_p": "p.Pro491Leu",
"transcript": "NM_001407246.1",
"protein_id": "NP_001394175.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 567,
"cds_start": 1472,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 2496,
"cdna_end": null,
"cdna_length": 3996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1472C>T",
"hgvs_p": "p.Pro491Leu",
"transcript": "ENST00000673903.1",
"protein_id": "ENSP00000501257.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 567,
"cds_start": 1472,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 1749,
"cdna_end": null,
"cdna_length": 3194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "c.1346C>T",
"hgvs_p": "p.Pro449Leu",
"transcript": "NM_001407247.1",
"protein_id": "NP_001394176.1",
"transcript_support_level": null,
"aa_start": 449,
"aa_end": null,
"aa_length": 525,
"cds_start": 1346,
"cds_end": null,
"cds_length": 1578,
"cdna_start": 1636,
"cdna_end": null,
"cdna_length": 3136,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.2393C>T",
"hgvs_p": null,
"transcript": "ENST00000490692.1",
"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": 3891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.*1343C>T",
"hgvs_p": null,
"transcript": "ENST00000673726.2",
"protein_id": "ENSP00000501004.1",
"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": 3849,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.*187C>T",
"hgvs_p": null,
"transcript": "ENST00000673913.2",
"protein_id": "ENSP00000501161.2",
"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": 3833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.*1291C>T",
"hgvs_p": null,
"transcript": "ENST00000713785.1",
"protein_id": "ENSP00000519087.1",
"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": 3424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.*1012C>T",
"hgvs_p": null,
"transcript": "ENST00000713787.1",
"protein_id": "ENSP00000519089.1",
"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": 3904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.2128C>T",
"hgvs_p": null,
"transcript": "NR_110451.3",
"protein_id": null,
"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": 3628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.1931C>T",
"hgvs_p": null,
"transcript": "NR_176318.1",
"protein_id": null,
"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": 3431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.2406C>T",
"hgvs_p": null,
"transcript": "NR_176319.1",
"protein_id": null,
"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": 3906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.2370C>T",
"hgvs_p": null,
"transcript": "NR_176320.1",
"protein_id": null,
"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": 3870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCSK9",
"gene_hgnc_id": 20001,
"hgvs_c": "n.2085C>T",
"hgvs_p": null,
"transcript": "NR_176321.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
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],
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"dbsnp": "rs755750316",
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"computational_score_selected": 0.051317691802978516,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.091,
"revel_prediction": "Benign",
"alphamissense_score": 0.0612,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.915,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_score": -4,
"acmg_classification": "Likely_benign",
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{
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"verdict": "Likely_benign",
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"effects": [
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"inheritance_mode": "AD,AR",
"hgvs_c": "c.1847C>T",
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],
"clinvar_disease": " 3, autosomal dominant,Familial hypercholesterolemia,Hypercholesterolemia",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Familial hypercholesterolemia|Hypercholesterolemia, autosomal dominant, 3",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}