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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: 7-4790698-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=4790698&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 10,
"criteria": [
"BP4",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "AP5Z1",
"hgnc_id": 22197,
"hgvs_c": "c.1964C>T",
"hgvs_p": "p.Ser655Leu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -10,
"transcript": "NM_014855.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6,BS1,BS2",
"acmg_score": -10,
"allele_count_reference_population": 803,
"alphamissense_prediction": null,
"alphamissense_score": 0.3189,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.11,
"chr": "7",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 48,Inborn genetic diseases,Retinal dystrophy,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:6 LB:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.39122575521469116,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 807,
"aa_ref": "S",
"aa_start": 655,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5529,
"cdna_start": 2057,
"cds_end": null,
"cds_length": 2424,
"cds_start": 1964,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_014855.3",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1964C>T",
"hgvs_p": "p.Ser655Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000649063.2",
"protein_coding": true,
"protein_id": "NP_055670.1",
"strand": true,
"transcript": "NM_014855.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 807,
"aa_ref": "S",
"aa_start": 655,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5529,
"cdna_start": 2057,
"cds_end": null,
"cds_length": 2424,
"cds_start": 1964,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000649063.2",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1964C>T",
"hgvs_p": "p.Ser655Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014855.3",
"protein_coding": true,
"protein_id": "ENSP00000497815.1",
"strand": true,
"transcript": "ENST00000649063.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 832,
"aa_ref": "S",
"aa_start": 680,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2956,
"cdna_start": 2121,
"cds_end": null,
"cds_length": 2499,
"cds_start": 2039,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000865634.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.2039C>T",
"hgvs_p": "p.Ser680Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535693.1",
"strand": true,
"transcript": "ENST00000865634.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 830,
"aa_ref": "S",
"aa_start": 678,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2939,
"cdna_start": 2115,
"cds_end": null,
"cds_length": 2493,
"cds_start": 2033,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000865636.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.2033C>T",
"hgvs_p": "p.Ser678Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535695.1",
"strand": true,
"transcript": "ENST00000865636.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 821,
"aa_ref": "S",
"aa_start": 669,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2901,
"cdna_start": 2077,
"cds_end": null,
"cds_length": 2466,
"cds_start": 2006,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000963395.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.2006C>T",
"hgvs_p": "p.Ser669Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633454.1",
"strand": true,
"transcript": "ENST00000963395.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 816,
"aa_ref": "S",
"aa_start": 664,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2919,
"cdna_start": 2084,
"cds_end": null,
"cds_length": 2451,
"cds_start": 1991,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000963389.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1991C>T",
"hgvs_p": "p.Ser664Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633448.1",
"strand": true,
"transcript": "ENST00000963389.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 814,
"aa_ref": "S",
"aa_start": 662,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2910,
"cdna_start": 2075,
"cds_end": null,
"cds_length": 2445,
"cds_start": 1985,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000963390.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1985C>T",
"hgvs_p": "p.Ser662Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633449.1",
"strand": true,
"transcript": "ENST00000963390.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 813,
"aa_ref": "S",
"aa_start": 661,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2878,
"cdna_start": 2053,
"cds_end": null,
"cds_length": 2442,
"cds_start": 1982,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000963393.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1982C>T",
"hgvs_p": "p.Ser661Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633452.1",
"strand": true,
"transcript": "ENST00000963393.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 806,
"aa_ref": "S",
"aa_start": 654,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2805,
"cdna_start": 1985,
"cds_end": null,
"cds_length": 2421,
"cds_start": 1961,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000963396.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1961C>T",
"hgvs_p": "p.Ser654Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633455.1",
"strand": true,
"transcript": "ENST00000963396.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 792,
"aa_ref": "S",
"aa_start": 640,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2835,
"cdna_start": 2008,
"cds_end": null,
"cds_length": 2379,
"cds_start": 1919,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000913390.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1919C>T",
"hgvs_p": "p.Ser640Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583449.1",
"strand": true,
"transcript": "ENST00000913390.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 791,
"aa_ref": "S",
"aa_start": 639,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2828,
"cdna_start": 2003,
"cds_end": null,
"cds_length": 2376,
"cds_start": 1916,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000963391.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1916C>T",
"hgvs_p": "p.Ser639Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633450.1",
"strand": true,
"transcript": "ENST00000963391.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 760,
"aa_ref": "S",
"aa_start": 608,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2732,
"cdna_start": 1905,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1823,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000865635.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1823C>T",
"hgvs_p": "p.Ser608Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535694.1",
"strand": true,
"transcript": "ENST00000865635.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 722,
"aa_ref": "S",
"aa_start": 570,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2616,
"cdna_start": 1791,
"cds_end": null,
"cds_length": 2169,
"cds_start": 1709,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000963392.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1709C>T",
"hgvs_p": "p.Ser570Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633451.1",
"strand": true,
"transcript": "ENST00000963392.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 651,
"aa_ref": "S",
"aa_start": 499,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5342,
"cdna_start": 1870,
"cds_end": null,
"cds_length": 1956,
"cds_start": 1496,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_001364858.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1496C>T",
"hgvs_p": "p.Ser499Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001351787.1",
"strand": true,
"transcript": "NM_001364858.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 492,
"aa_ref": "S",
"aa_start": 340,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1915,
"cdna_start": 1088,
"cds_end": null,
"cds_length": 1479,
"cds_start": 1019,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000963394.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1019C>T",
"hgvs_p": "p.Ser340Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633453.1",
"strand": true,
"transcript": "ENST00000963394.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 695,
"aa_ref": "S",
"aa_start": 543,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5234,
"cdna_start": 1762,
"cds_end": null,
"cds_length": 2088,
"cds_start": 1628,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_047421098.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1628C>T",
"hgvs_p": "p.Ser543Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047277054.1",
"strand": true,
"transcript": "XM_047421098.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 691,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2521,
"cdna_start": null,
"cds_end": null,
"cds_length": 2076,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000865637.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.1806-417C>T",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535696.1",
"strand": true,
"transcript": "ENST00000865637.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 317,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1299,
"cdna_start": null,
"cds_end": null,
"cds_length": 954,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650581.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.606-112C>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000497156.1",
"strand": true,
"transcript": "ENST00000650581.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 144,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 917,
"cdna_start": null,
"cds_end": null,
"cds_length": 435,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648237.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "c.225+107C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000497377.1",
"strand": true,
"transcript": "ENST00000648237.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2337,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000469614.1",
"gene_hgnc_id": 22197,
"gene_symbol": "AP5Z1",
"hgvs_c": "n.1512C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000469614.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3078,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
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