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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-78011674-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=78011674&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 78011674,
"ref": "G",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000341514.11",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "NM_000052.7",
"protein_id": "NP_000043.4",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1500,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 2336,
"cdna_end": null,
"cdna_length": 8492,
"mane_select": "ENST00000341514.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000341514.11",
"protein_id": "ENSP00000345728.6",
"transcript_support_level": 1,
"aa_start": 724,
"aa_end": null,
"aa_length": 1500,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 2336,
"cdna_end": null,
"cdna_length": 8492,
"mane_select": "NM_000052.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2265G>T",
"hgvs_p": "p.Gln755His",
"transcript": "ENST00000689767.1",
"protein_id": "ENSP00000509406.1",
"transcript_support_level": null,
"aa_start": 755,
"aa_end": null,
"aa_length": 1531,
"cds_start": 2265,
"cds_end": null,
"cds_length": 4596,
"cdna_start": 2413,
"cdna_end": null,
"cdna_length": 8569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2202G>T",
"hgvs_p": "p.Gln734His",
"transcript": "ENST00000343533.10",
"protein_id": "ENSP00000343026.6",
"transcript_support_level": 5,
"aa_start": 734,
"aa_end": null,
"aa_length": 1510,
"cds_start": 2202,
"cds_end": null,
"cds_length": 4533,
"cdna_start": 2392,
"cdna_end": null,
"cdna_length": 8548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000685264.1",
"protein_id": "ENSP00000510136.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1500,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 2364,
"cdna_end": null,
"cdna_length": 4984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000686133.1",
"protein_id": "ENSP00000509233.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1500,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 2343,
"cdna_end": null,
"cdna_length": 5003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000687086.1",
"protein_id": "ENSP00000509566.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1500,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 2485,
"cdna_end": null,
"cdna_length": 5092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000686033.1",
"protein_id": "ENSP00000510693.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1435,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4308,
"cdna_start": 2290,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "NM_001282224.2",
"protein_id": "NP_001269153.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1422,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4269,
"cdna_start": 2336,
"cdna_end": null,
"cdna_length": 8258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000686543.1",
"protein_id": "ENSP00000509477.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1422,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4269,
"cdna_start": 2290,
"cdna_end": null,
"cdna_length": 4716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000692908.1",
"protein_id": "ENSP00000508627.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1422,
"cds_start": 2172,
"cds_end": null,
"cds_length": 4269,
"cdna_start": 2482,
"cdna_end": null,
"cdna_length": 4908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000689530.1",
"protein_id": "ENSP00000509707.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 971,
"cds_start": 2172,
"cds_end": null,
"cds_length": 2916,
"cdna_start": 2506,
"cdna_end": null,
"cdna_length": 3250,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000686688.1",
"protein_id": "ENSP00000509416.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 929,
"cds_start": 2172,
"cds_end": null,
"cds_length": 2790,
"cdna_start": 2334,
"cdna_end": null,
"cdna_length": 3050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000693398.1",
"protein_id": "ENSP00000510089.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 929,
"cds_start": 2172,
"cds_end": null,
"cds_length": 2790,
"cdna_start": 2288,
"cdna_end": null,
"cdna_length": 3000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000689649.1",
"protein_id": "ENSP00000509277.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 844,
"cds_start": 2172,
"cds_end": null,
"cds_length": 2535,
"cdna_start": 2290,
"cdna_end": null,
"cdna_length": 3268,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2172G>T",
"hgvs_p": "p.Gln724His",
"transcript": "ENST00000686480.1",
"protein_id": "ENSP00000508978.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 766,
"cds_start": 2172,
"cds_end": null,
"cds_length": 2301,
"cdna_start": 2290,
"cdna_end": null,
"cdna_length": 3115,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.2088G>T",
"hgvs_p": "p.Gln696His",
"transcript": "ENST00000692110.1",
"protein_id": "ENSP00000509366.1",
"transcript_support_level": null,
"aa_start": 696,
"aa_end": null,
"aa_length": 695,
"cds_start": 2088,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 2202,
"cdna_end": null,
"cdna_length": 2202,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.*2086G>T",
"hgvs_p": null,
"transcript": "ENST00000645094.1",
"protein_id": "ENSP00000493605.1",
"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": 4019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.823G>T",
"hgvs_p": null,
"transcript": "ENST00000682475.1",
"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": 6274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.1203G>T",
"hgvs_p": null,
"transcript": "ENST00000686255.1",
"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": 7359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.2312G>T",
"hgvs_p": null,
"transcript": "ENST00000686515.1",
"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": 2605,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.2483G>T",
"hgvs_p": null,
"transcript": "ENST00000686999.1",
"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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}
],
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"computational_score_selected": 0.8859694004058838,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
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"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
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"revel_prediction": "Pathogenic",
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"bayesdelnoaf_score": 0.72,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.86,
"spliceai_max_prediction": "Pathogenic",
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"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
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"acmg_by_gene": [
{
"score": 8,
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"pathogenic_score": 8,
"criteria": [
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"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000341514.11",
"gene_symbol": "ATP7A",
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"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "XL,AD",
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"hgvs_p": "p.Gln724His"
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{
"score": 6,
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"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
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"effects": [
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],
"inheritance_mode": "XL",
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}
],
"clinvar_disease": "Menkes kinky-hair syndrome",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Menkes kinky-hair syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}