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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-154031402-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=154031402&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 154031402,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001110792.2",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Phe154Phe",
"transcript": "NM_001110792.2",
"protein_id": "NP_001104262.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 498,
"cds_start": 462,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 514,
"cdna_end": null,
"cdna_length": 10343,
"mane_select": "ENST00000453960.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Phe154Phe",
"transcript": "ENST00000453960.7",
"protein_id": "ENSP00000395535.2",
"transcript_support_level": 1,
"aa_start": 154,
"aa_end": null,
"aa_length": 498,
"cds_start": 462,
"cds_end": null,
"cds_length": 1497,
"cdna_start": 514,
"cdna_end": null,
"cdna_length": 10343,
"mane_select": "NM_001110792.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.426C>T",
"hgvs_p": "p.Phe142Phe",
"transcript": "NM_004992.4",
"protein_id": "NP_004983.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 486,
"cds_start": 426,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 10467,
"mane_select": null,
"mane_plus": "ENST00000303391.11",
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.426C>T",
"hgvs_p": "p.Phe142Phe",
"transcript": "ENST00000303391.11",
"protein_id": "ENSP00000301948.6",
"transcript_support_level": 1,
"aa_start": 142,
"aa_end": null,
"aa_length": 486,
"cds_start": 426,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 638,
"cdna_end": null,
"cdna_length": 10467,
"mane_select": null,
"mane_plus": "NM_004992.4",
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.-135C>T",
"hgvs_p": null,
"transcript": "NM_001386137.1",
"protein_id": "NP_001373066.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 263,
"cds_start": -4,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.-135C>T",
"hgvs_p": null,
"transcript": "NM_001386138.1",
"protein_id": "NP_001373067.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 263,
"cds_start": -4,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10358,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.-135C>T",
"hgvs_p": null,
"transcript": "NM_001386139.1",
"protein_id": "NP_001373068.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 263,
"cds_start": -4,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.-135C>T",
"hgvs_p": null,
"transcript": "XM_047442122.1",
"protein_id": "XP_047298078.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 263,
"cds_start": -4,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.426C>T",
"hgvs_p": "p.Phe142Phe",
"transcript": "ENST00000630151.3",
"protein_id": "ENSP00000486089.2",
"transcript_support_level": 5,
"aa_start": 142,
"aa_end": null,
"aa_length": 486,
"cds_start": 426,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 623,
"cdna_end": null,
"cdna_length": 10452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.147C>T",
"hgvs_p": "p.Phe49Phe",
"transcript": "NM_001316337.2",
"protein_id": "NP_001303266.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 393,
"cds_start": 147,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 806,
"cdna_end": null,
"cdna_length": 10635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.147C>T",
"hgvs_p": "p.Phe49Phe",
"transcript": "NM_001369391.2",
"protein_id": "NP_001356320.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 393,
"cds_start": 147,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 1101,
"cdna_end": null,
"cdna_length": 10930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.147C>T",
"hgvs_p": "p.Phe49Phe",
"transcript": "NM_001369392.2",
"protein_id": "NP_001356321.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 393,
"cds_start": 147,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 750,
"cdna_end": null,
"cdna_length": 10579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.147C>T",
"hgvs_p": "p.Phe49Phe",
"transcript": "NM_001369393.2",
"protein_id": "NP_001356322.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 393,
"cds_start": 147,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 626,
"cdna_end": null,
"cdna_length": 10455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.147C>T",
"hgvs_p": "p.Phe49Phe",
"transcript": "NM_001369394.2",
"protein_id": "NP_001356323.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 393,
"cds_start": 147,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 557,
"cdna_end": null,
"cdna_length": 10386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.426C>T",
"hgvs_p": "p.Phe142Phe",
"transcript": "ENST00000637917.2",
"protein_id": "ENSP00000489847.2",
"transcript_support_level": 5,
"aa_start": 142,
"aa_end": null,
"aa_length": 333,
"cds_start": 426,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 658,
"cdna_end": null,
"cdna_length": 1298,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.462C>T",
"hgvs_p": "p.Phe154Phe",
"transcript": "ENST00000407218.5",
"protein_id": "ENSP00000384865.2",
"transcript_support_level": 5,
"aa_start": 154,
"aa_end": null,
"aa_length": 184,
"cds_start": 462,
"cds_end": null,
"cds_length": 555,
"cdna_start": 486,
"cdna_end": null,
"cdna_length": 1174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.426C>T",
"hgvs_p": "p.Phe142Phe",
"transcript": "ENST00000415944.4",
"protein_id": "ENSP00000416267.2",
"transcript_support_level": 5,
"aa_start": 142,
"aa_end": null,
"aa_length": 172,
"cds_start": 426,
"cds_end": null,
"cds_length": 519,
"cdna_start": 848,
"cdna_end": null,
"cdna_length": 1907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.426C>T",
"hgvs_p": "p.Phe142Phe",
"transcript": "ENST00000628176.2",
"protein_id": "ENSP00000486978.1",
"transcript_support_level": 3,
"aa_start": 142,
"aa_end": null,
"aa_length": 172,
"cds_start": 426,
"cds_end": null,
"cds_length": 519,
"cdna_start": 658,
"cdna_end": null,
"cdna_length": 1712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.426C>T",
"hgvs_p": "p.Phe142Phe",
"transcript": "XM_047442115.1",
"protein_id": "XP_047298071.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 486,
"cds_start": 426,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 1766,
"cdna_end": null,
"cdna_length": 11595,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.426C>T",
"hgvs_p": "p.Phe142Phe",
"transcript": "XM_047442116.1",
"protein_id": "XP_047298072.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 486,
"cds_start": 426,
"cds_end": null,
"cds_length": 1461,
"cdna_start": 2928,
"cdna_end": null,
"cdna_length": 12757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.147C>T",
"hgvs_p": "p.Phe49Phe",
"transcript": "XM_024452383.2",
"protein_id": "XP_024308151.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 393,
"cds_start": 147,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 2303,
"cdna_end": null,
"cdna_length": 12132,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECP2",
"gene_hgnc_id": 6990,
"hgvs_c": "c.147C>T",
"hgvs_p": "p.Phe49Phe",
"transcript": "XM_047442117.1",
"protein_id": "XP_047298073.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 393,
"cds_start": 147,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 944,
"cdna_end": null,
"cdna_length": 10773,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
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],
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"computational_score_selected": -0.46000000834465027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"alphamissense_score": null,
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"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.854,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"acmg_score": -14,
"acmg_classification": "Benign",
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"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
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"BS2"
],
"verdict": "Benign",
"transcript": "NM_001110792.2",
"gene_symbol": "MECP2",
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"effects": [
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],
"inheritance_mode": "XL,Unknown,AD",
"hgvs_c": "c.462C>T",
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],
"clinvar_disease": "Inborn genetic diseases,Rett syndrome,Severe neonatal-onset encephalopathy with microcephaly,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:5",
"phenotype_combined": "not specified|Severe neonatal-onset encephalopathy with microcephaly|not provided|Inborn genetic diseases|Rett syndrome",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}