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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: X-54017674-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=54017674&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 54017674,
"ref": "A",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_015107.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "NM_015107.3",
"protein_id": "NP_055922.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 1024,
"cds_start": 441,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 6357,
"mane_select": "ENST00000338154.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "ENST00000338154.11",
"protein_id": "ENSP00000338868.6",
"transcript_support_level": 1,
"aa_start": 147,
"aa_end": null,
"aa_length": 1024,
"cds_start": 441,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 6357,
"mane_select": "NM_015107.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.549T>A",
"hgvs_p": "p.Val183Val",
"transcript": "ENST00000357988.9",
"protein_id": "ENSP00000350676.5",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 1060,
"cds_start": 549,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 908,
"cdna_end": null,
"cdna_length": 6024,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "ENST00000322659.12",
"protein_id": "ENSP00000319473.8",
"transcript_support_level": 1,
"aa_start": 147,
"aa_end": null,
"aa_length": 878,
"cds_start": 441,
"cds_end": null,
"cds_length": 2637,
"cdna_start": 617,
"cdna_end": null,
"cdna_length": 2921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.549T>A",
"hgvs_p": "p.Val183Val",
"transcript": "NM_001184896.1",
"protein_id": "NP_001171825.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 1060,
"cds_start": 549,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 5907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "ENST00000396282.7",
"protein_id": "ENSP00000379578.3",
"transcript_support_level": 5,
"aa_start": 147,
"aa_end": null,
"aa_length": 1049,
"cds_start": 441,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.549T>A",
"hgvs_p": "p.Val183Val",
"transcript": "NM_001441096.1",
"protein_id": "NP_001428025.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 984,
"cds_start": 549,
"cds_end": null,
"cds_length": 2955,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "NM_001184897.2",
"protein_id": "NP_001171826.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 948,
"cds_start": 441,
"cds_end": null,
"cds_length": 2847,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 4952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.549T>A",
"hgvs_p": "p.Val183Val",
"transcript": "NM_001441097.1",
"protein_id": "NP_001428026.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 931,
"cds_start": 549,
"cds_end": null,
"cds_length": 2796,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 3791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "ENST00000338946.11",
"protein_id": "ENSP00000340051.7",
"transcript_support_level": 2,
"aa_start": 147,
"aa_end": null,
"aa_length": 923,
"cds_start": 441,
"cds_end": null,
"cds_length": 2772,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 5236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "NM_001184898.2",
"protein_id": "NP_001171827.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 878,
"cds_start": 441,
"cds_end": null,
"cds_length": 2637,
"cdna_start": 570,
"cdna_end": null,
"cdna_length": 3515,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.549T>A",
"hgvs_p": "p.Val183Val",
"transcript": "NM_001441098.1",
"protein_id": "NP_001428027.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 830,
"cds_start": 549,
"cds_end": null,
"cds_length": 2493,
"cdna_start": 795,
"cdna_end": null,
"cdna_length": 3488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.549T>A",
"hgvs_p": "p.Val183Val",
"transcript": "XM_005261996.2",
"protein_id": "XP_005262053.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 1085,
"cds_start": 549,
"cds_end": null,
"cds_length": 3258,
"cdna_start": 640,
"cdna_end": null,
"cdna_length": 4650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.549T>A",
"hgvs_p": "p.Val183Val",
"transcript": "XM_011530778.2",
"protein_id": "XP_011529080.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 1085,
"cds_start": 549,
"cds_end": null,
"cds_length": 3258,
"cdna_start": 698,
"cdna_end": null,
"cdna_length": 4708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.549T>A",
"hgvs_p": "p.Val183Val",
"transcript": "XM_047441934.1",
"protein_id": "XP_047297890.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 1060,
"cds_start": 549,
"cds_end": null,
"cds_length": 3183,
"cdna_start": 670,
"cdna_end": null,
"cdna_length": 5782,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "XM_005261999.2",
"protein_id": "XP_005262056.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 1049,
"cds_start": 441,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 1896,
"cdna_end": null,
"cdna_length": 5906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val",
"transcript": "XM_047441935.1",
"protein_id": "XP_047297891.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 1049,
"cds_start": 441,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 603,
"cdna_end": null,
"cdna_length": 4613,
"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": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "n.441T>A",
"hgvs_p": null,
"transcript": "ENST00000686349.1",
"protein_id": "ENSP00000510424.1",
"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": 6524,
"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": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "n.441T>A",
"hgvs_p": null,
"transcript": "ENST00000687764.1",
"protein_id": "ENSP00000509967.1",
"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": 6476,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "n.147+4585T>A",
"hgvs_p": null,
"transcript": "ENST00000691629.1",
"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": 4903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.*105T>A",
"hgvs_p": null,
"transcript": "ENST00000453905.5",
"protein_id": "ENSP00000405897.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 147,
"cds_start": -4,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.*63T>A",
"hgvs_p": null,
"transcript": "ENST00000425862.5",
"protein_id": "ENSP00000408113.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 125,
"cds_start": -4,
"cds_end": null,
"cds_length": 378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF8",
"gene_hgnc_id": 20672,
"hgvs_c": "c.*96T>A",
"hgvs_p": null,
"transcript": "ENST00000437224.5",
"protein_id": "ENSP00000398995.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": -4,
"cds_end": null,
"cds_length": 345,
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},
{
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"canonical": false,
"protein_coding": true,
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"downstream_gene_variant"
],
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"exon_count": 5,
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"gene_symbol": "PHF8",
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"protein_id": "ENSP00000404117.1",
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}
],
"gene_symbol": "PHF8",
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"dbsnp": "rs148215758",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"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": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.008,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
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"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_015107.3",
"gene_symbol": "PHF8",
"hgnc_id": 20672,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.441T>A",
"hgvs_p": "p.Val147Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}