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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: 2-227008112-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227008112&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227008112,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000396625.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "NM_000092.5",
"protein_id": "NP_000083.3",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1690,
"cds_start": 4715,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 9984,
"mane_select": "ENST00000396625.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "ENST00000396625.5",
"protein_id": "ENSP00000379866.3",
"transcript_support_level": 5,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1690,
"cds_start": 4715,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 9984,
"mane_select": "NM_000092.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.317C>T",
"hgvs_p": "p.Pro106Leu",
"transcript": "ENST00000682098.1",
"protein_id": "ENSP00000508331.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 224,
"cds_start": 317,
"cds_end": null,
"cds_length": 675,
"cdna_start": 317,
"cdna_end": null,
"cdna_length": 675,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_005246281.4",
"protein_id": "XP_005246338.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1690,
"cds_start": 4715,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 4909,
"cdna_end": null,
"cdna_length": 9878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_047443228.1",
"protein_id": "XP_047299184.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1690,
"cds_start": 4715,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 4892,
"cdna_end": null,
"cdna_length": 9861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4634C>T",
"hgvs_p": "p.Pro1545Leu",
"transcript": "XM_011510557.3",
"protein_id": "XP_011508859.1",
"transcript_support_level": null,
"aa_start": 1545,
"aa_end": null,
"aa_length": 1663,
"cds_start": 4634,
"cds_end": null,
"cds_length": 4992,
"cdna_start": 4934,
"cdna_end": null,
"cdna_length": 9903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4607C>T",
"hgvs_p": "p.Pro1536Leu",
"transcript": "XM_011510558.3",
"protein_id": "XP_011508860.1",
"transcript_support_level": null,
"aa_start": 1536,
"aa_end": null,
"aa_length": 1654,
"cds_start": 4607,
"cds_end": null,
"cds_length": 4965,
"cdna_start": 4907,
"cdna_end": null,
"cdna_length": 9876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4598C>T",
"hgvs_p": "p.Pro1533Leu",
"transcript": "XM_017003297.2",
"protein_id": "XP_016858786.1",
"transcript_support_level": null,
"aa_start": 1533,
"aa_end": null,
"aa_length": 1651,
"cds_start": 4598,
"cds_end": null,
"cds_length": 4956,
"cdna_start": 4898,
"cdna_end": null,
"cdna_length": 9867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4526C>T",
"hgvs_p": "p.Pro1509Leu",
"transcript": "XM_006712246.4",
"protein_id": "XP_006712309.1",
"transcript_support_level": null,
"aa_start": 1509,
"aa_end": null,
"aa_length": 1627,
"cds_start": 4526,
"cds_end": null,
"cds_length": 4884,
"cdna_start": 4826,
"cdna_end": null,
"cdna_length": 9795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_011510559.3",
"protein_id": "XP_011508861.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1612,
"cds_start": 4715,
"cds_end": null,
"cds_length": 4839,
"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 6050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_011510560.3",
"protein_id": "XP_011508862.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1612,
"cds_start": 4715,
"cds_end": null,
"cds_length": 4839,
"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 6027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_047443241.1",
"protein_id": "XP_047299197.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1612,
"cds_start": 4715,
"cds_end": null,
"cds_length": 4839,
"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 6272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_047443242.1",
"protein_id": "XP_047299198.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1612,
"cds_start": 4715,
"cds_end": null,
"cds_length": 4839,
"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 6249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_011510561.3",
"protein_id": "XP_011508863.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1608,
"cds_start": 4715,
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"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 5688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_011510562.3",
"protein_id": "XP_011508864.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1608,
"cds_start": 4715,
"cds_end": null,
"cds_length": 4827,
"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 8448,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 47,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu",
"transcript": "XM_047443245.1",
"protein_id": "XP_047299201.1",
"transcript_support_level": null,
"aa_start": 1572,
"aa_end": null,
"aa_length": 1608,
"cds_start": 4715,
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"cdna_start": 5015,
"cdna_end": null,
"cdna_length": 5488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.4160C>T",
"hgvs_p": "p.Pro1387Leu",
"transcript": "XM_005246282.4",
"protein_id": "XP_005246339.1",
"transcript_support_level": null,
"aa_start": 1387,
"aa_end": null,
"aa_length": 1505,
"cds_start": 4160,
"cds_end": null,
"cds_length": 4518,
"cdna_start": 4460,
"cdna_end": null,
"cdna_length": 9429,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.3041C>T",
"hgvs_p": "p.Pro1014Leu",
"transcript": "XM_011510572.4",
"protein_id": "XP_011508874.1",
"transcript_support_level": null,
"aa_start": 1014,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3041,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 3268,
"cdna_end": null,
"cdna_length": 8237,
"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": 47,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "n.5015C>T",
"hgvs_p": null,
"transcript": "XR_001738602.2",
"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": 6137,
"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": 47,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "n.5015C>T",
"hgvs_p": null,
"transcript": "XR_007069255.1",
"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,
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"cdna_length": 5981,
"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": 47,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "n.5015C>T",
"hgvs_p": null,
"transcript": "XR_922837.3",
"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": 5846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.*48C>T",
"hgvs_p": null,
"transcript": "XM_047443246.1",
"protein_id": "XP_047299202.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1470,
"cds_start": -4,
"cds_end": null,
"cds_length": 4413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": 44,
"intron_rank_end": null,
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],
"gene_symbol": "COL4A4",
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"dbsnp": "rs121912863",
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"hom_count_reference_population": 2,
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"gnomad_exomes_af": 0.000125206,
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"computational_score_selected": 0.617181122303009,
"computational_prediction_selected": "Uncertain_significance",
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"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.721,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1106,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.792,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_score": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS1_Supporting",
"acmg_by_gene": [
{
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"pathogenic_score": 0,
"criteria": [
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000396625.5",
"gene_symbol": "COL4A4",
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"effects": [
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"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.4715C>T",
"hgvs_p": "p.Pro1572Leu"
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],
"clinvar_disease": " 1, benign familial,Alport syndrome,Autosomal recessive Alport syndrome,COL4A4-related disorder,Hematuria,Inborn genetic diseases,Kidney disorder,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:2 US:8 LB:1",
"phenotype_combined": "Autosomal recessive Alport syndrome|not provided|Kidney disorder|not specified|Alport syndrome|Inborn genetic diseases|COL4A4-related disorder|Hematuria, benign familial, 1;Autosomal recessive Alport syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}