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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: 17-58206456-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=58206456&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 58206456,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000393119.7",
"consequences": [
{
"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": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1490+9C>T",
"hgvs_p": null,
"transcript": "NM_017777.4",
"protein_id": "NP_060247.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 559,
"cds_start": -4,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2343,
"mane_select": "ENST00000393119.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1490+9C>T",
"hgvs_p": null,
"transcript": "ENST00000393119.7",
"protein_id": "ENSP00000376827.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 559,
"cds_start": -4,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2343,
"mane_select": "NM_017777.4",
"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": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1061+9C>T",
"hgvs_p": null,
"transcript": "ENST00000537529.7",
"protein_id": "ENSP00000442096.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 416,
"cds_start": -4,
"cds_end": null,
"cds_length": 1251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2083,
"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": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.2736C>T",
"hgvs_p": null,
"transcript": "ENST00000677416.1",
"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": 3639,
"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": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1408-76C>T",
"hgvs_p": null,
"transcript": "NM_001321269.2",
"protein_id": "NP_001308198.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 561,
"cds_start": -4,
"cds_end": null,
"cds_length": 1686,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2260,
"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": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1408-76C>T",
"hgvs_p": null,
"transcript": "ENST00000678463.1",
"protein_id": "ENSP00000502984.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 561,
"cds_start": -4,
"cds_end": null,
"cds_length": 1686,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2260,
"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": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1361+9C>T",
"hgvs_p": null,
"transcript": "ENST00000676787.1",
"protein_id": "ENSP00000503999.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 516,
"cds_start": -4,
"cds_end": null,
"cds_length": 1551,
"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": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1274-76C>T",
"hgvs_p": null,
"transcript": "NM_001330397.2",
"protein_id": "NP_001317326.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 456,
"cds_start": -4,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2126,
"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": 16,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1274-76C>T",
"hgvs_p": null,
"transcript": "ENST00000313863.11",
"protein_id": "ENSP00000316631.6",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 456,
"cds_start": -4,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2126,
"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": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.881+9C>T",
"hgvs_p": null,
"transcript": "NM_001321268.2",
"protein_id": "NP_001308197.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 356,
"cds_start": -4,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2245,
"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": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.*897+9C>T",
"hgvs_p": null,
"transcript": "ENST00000393120.6",
"protein_id": "ENSP00000376828.2",
"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": 1926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.316+9C>T",
"hgvs_p": null,
"transcript": "ENST00000583577.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.*1109+9C>T",
"hgvs_p": null,
"transcript": "ENST00000675753.2",
"protein_id": "ENSP00000502156.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.*964+9C>T",
"hgvs_p": null,
"transcript": "ENST00000677111.1",
"protein_id": "ENSP00000504282.1",
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},
{
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"strand": false,
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"intron_variant"
],
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"exon_count": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.2764+9C>T",
"hgvs_p": null,
"transcript": "ENST00000677160.1",
"protein_id": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.*834+9C>T",
"hgvs_p": null,
"transcript": "ENST00000677486.1",
"protein_id": "ENSP00000503852.1",
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},
{
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],
"exon_rank": null,
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"gene_symbol": "MKS1",
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"hgvs_c": "n.2190+9C>T",
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"transcript": "ENST00000677709.1",
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"biotype": null,
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 16,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.2390+9C>T",
"hgvs_p": null,
"transcript": "ENST00000678011.1",
"protein_id": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
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],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.*1264+9C>T",
"hgvs_p": null,
"transcript": "ENST00000678432.1",
"protein_id": "ENSP00000504452.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 13,
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"gene_symbol": "MKS1",
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"hgvs_c": "n.*815-76C>T",
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"transcript": "ENST00000678568.1",
"protein_id": "ENSP00000504754.1",
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},
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"strand": false,
"consequences": [
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],
"exon_rank": null,
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"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "MKS1",
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"hgvs_c": "n.*834+9C>T",
"hgvs_p": null,
"transcript": "ENST00000678641.1",
"protein_id": "ENSP00000503159.1",
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},
{
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "n.1805+9C>T",
"hgvs_p": null,
"transcript": "ENST00000678763.1",
"protein_id": null,
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"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_length": 2633,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"hgvs_c": "c.1417-76C>T",
"hgvs_p": null,
"transcript": "XM_011524957.3",
"protein_id": "XP_011523259.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 564,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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},
{
"aa_ref": null,
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"intron_variant"
],
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"gene_symbol": "MKS1",
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"hgvs_c": "c.979-76C>T",
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"transcript": "XM_005257485.5",
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},
{
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"protein_coding": true,
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"intron_variant"
],
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"gene_symbol": "MKS1",
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"hgvs_c": "c.799-76C>T",
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"transcript": "XM_047436333.1",
"protein_id": "XP_047292289.1",
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"aa_length": 358,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1797,
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"feature": null
}
],
"gene_symbol": "MKS1",
"gene_hgnc_id": 7121,
"dbsnp": "rs1555596804",
"frequency_reference_population": 0.0000013681107,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136811,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6299999952316284,
"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": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.956,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000393119.7",
"gene_symbol": "MKS1",
"hgnc_id": 7121,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1490+9C>T",
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}
],
"clinvar_disease": "Joubert syndrome,Meckel-Gruber syndrome",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Joubert syndrome;Meckel-Gruber syndrome",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}