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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: 2-227254099-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227254099&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227254099,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000396578.8",
"consequences": [
{
"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": 52,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.766-13G>A",
"hgvs_p": null,
"transcript": "NM_000091.5",
"protein_id": "NP_000082.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1670,
"cds_start": -4,
"cds_end": null,
"cds_length": 5013,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8038,
"mane_select": "ENST00000396578.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.766-13G>A",
"hgvs_p": null,
"transcript": "ENST00000396578.8",
"protein_id": "ENSP00000379823.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1670,
"cds_start": -4,
"cds_end": null,
"cds_length": 5013,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8038,
"mane_select": "NM_000091.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1592+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000439598.6",
"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": 2568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1658+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000396588.6",
"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": 2214,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.4606+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000433324.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 6087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1331+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000437673.6",
"protein_id": null,
"transcript_support_level": 3,
"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": 1474,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1211+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000606119.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 2692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1346+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000656707.1",
"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": 2827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1552+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000656771.1",
"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": 3037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1606+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000657158.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 3087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1446+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000657873.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1549+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000662009.1",
"protein_id": null,
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
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"hgvs_c": "n.1356+5079C>T",
"hgvs_p": null,
"transcript": "ENST00000665165.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 7,
"intron_rank": 6,
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"gene_symbol": "MFF-DT",
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"hgvs_c": "n.1855+5079C>T",
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"transcript": "ENST00000665988.1",
"protein_id": null,
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},
{
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],
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"gene_symbol": "MFF-DT",
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"transcript": "ENST00000666788.1",
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.4167+5079C>T",
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"transcript": "ENST00000668704.1",
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},
{
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],
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"gene_symbol": "MFF-DT",
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},
{
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"strand": false,
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],
"exon_rank": null,
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"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1765-2860C>T",
"hgvs_p": null,
"transcript": "ENST00000671563.1",
"protein_id": null,
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "MFF-DT",
"gene_hgnc_id": 41067,
"hgvs_c": "n.1592+5079C>T",
"hgvs_p": null,
"transcript": "NR_102371.1",
"protein_id": null,
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},
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],
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"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.766-13G>A",
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"transcript": "XM_005246277.4",
"protein_id": "XP_005246334.1",
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},
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"strand": true,
"consequences": [
"intron_variant"
],
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"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
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"hgvs_c": "c.766-13G>A",
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"transcript": "XM_011510555.2",
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},
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"strand": true,
"consequences": [
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],
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"intron_rank": 13,
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"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.766-13G>A",
"hgvs_p": null,
"transcript": "XM_047443224.1",
"protein_id": "XP_047299180.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 43,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.766-13G>A",
"hgvs_p": null,
"transcript": "XM_006712245.4",
"protein_id": "XP_006712308.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1189,
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"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 39,
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"gene_symbol": "COL4A3",
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"hgvs_c": "c.766-13G>A",
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"transcript": "XM_017003295.2",
"protein_id": "XP_016858784.1",
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"aa_start": null,
"aa_end": null,
"aa_length": 1119,
"cds_start": -4,
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"cds_length": 3360,
"cdna_start": null,
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"cdna_length": 3898,
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"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
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"exon_count": 38,
"intron_rank": 13,
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"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.766-13G>A",
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"transcript": "XM_005246280.4",
"protein_id": "XP_005246337.1",
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"aa_start": null,
"aa_end": null,
"aa_length": 1051,
"cds_start": -4,
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"cds_length": 3156,
"cdna_start": null,
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"cdna_length": 3357,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 42,
"intron_rank": 13,
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"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "n.869-13G>A",
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"transcript": "XR_001738601.2",
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"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": 4938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"dbsnp": "rs77431913",
"frequency_reference_population": 0.012350027,
"hom_count_reference_population": 915,
"allele_count_reference_population": 19914,
"gnomad_exomes_af": 0.0104686,
"gnomad_genomes_af": 0.0304008,
"gnomad_exomes_ac": 15287,
"gnomad_genomes_ac": 4627,
"gnomad_exomes_homalt": 718,
"gnomad_genomes_homalt": 197,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.12,
"phylop100way_prediction": "Benign",
"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": -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": "ENST00000396578.8",
"gene_symbol": "COL4A3",
"hgnc_id": 2204,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.766-13G>A",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000439598.6",
"gene_symbol": "MFF-DT",
"hgnc_id": 41067,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1592+5079C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Alport syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Alport syndrome|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}