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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: 14-72974821-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=72974821&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 3,
"criteria": [
"PM2",
"BP4_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "ZFYVE1",
"hgnc_id": 13180,
"hgvs_c": "c.1945C>A",
"hgvs_p": "p.Arg649Arg",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -1,
"transcript": "NM_021260.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP7",
"acmg_score": -1,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"chr": "14",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.30000001192092896,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 777,
"aa_ref": "R",
"aa_start": 649,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4380,
"cdna_start": 2560,
"cds_end": null,
"cds_length": 2334,
"cds_start": 1945,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_021260.4",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1945C>A",
"hgvs_p": "p.Arg649Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000556143.6",
"protein_coding": true,
"protein_id": "NP_067083.1",
"strand": false,
"transcript": "NM_021260.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 777,
"aa_ref": "R",
"aa_start": 649,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4380,
"cdna_start": 2560,
"cds_end": null,
"cds_length": 2334,
"cds_start": 1945,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000556143.6",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1945C>A",
"hgvs_p": "p.Arg649Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_021260.4",
"protein_coding": true,
"protein_id": "ENSP00000450742.1",
"strand": false,
"transcript": "ENST00000556143.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 763,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4362,
"cdna_start": 2543,
"cds_end": null,
"cds_length": 2292,
"cds_start": 1903,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000318876.9",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1903C>A",
"hgvs_p": "p.Arg635Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000326921.5",
"strand": false,
"transcript": "ENST00000318876.9",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 362,
"aa_ref": "R",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1225,
"cdna_start": 836,
"cds_end": null,
"cds_length": 1089,
"cds_start": 700,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000555072.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.700C>A",
"hgvs_p": "p.Arg234Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452232.1",
"strand": false,
"transcript": "ENST00000555072.1",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 789,
"aa_ref": "R",
"aa_start": 649,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3244,
"cdna_start": 2560,
"cds_end": null,
"cds_length": 2370,
"cds_start": 1945,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000553891.5",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1945C>A",
"hgvs_p": "p.Arg649Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452442.1",
"strand": false,
"transcript": "ENST00000553891.5",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 783,
"aa_ref": "R",
"aa_start": 655,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4026,
"cdna_start": 2578,
"cds_end": null,
"cds_length": 2352,
"cds_start": 1963,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000864218.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1963C>A",
"hgvs_p": "p.Arg655Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534277.1",
"strand": false,
"transcript": "ENST00000864218.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 777,
"aa_ref": "R",
"aa_start": 649,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2847,
"cdna_start": 2453,
"cds_end": null,
"cds_length": 2334,
"cds_start": 1945,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000864219.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1945C>A",
"hgvs_p": "p.Arg649Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534278.1",
"strand": false,
"transcript": "ENST00000864219.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 766,
"aa_ref": "R",
"aa_start": 638,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2862,
"cdna_start": 2468,
"cds_end": null,
"cds_length": 2301,
"cds_start": 1912,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000864220.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1912C>A",
"hgvs_p": "p.Arg638Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534279.1",
"strand": false,
"transcript": "ENST00000864220.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 763,
"aa_ref": "R",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4338,
"cdna_start": 2518,
"cds_end": null,
"cds_length": 2292,
"cds_start": 1903,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001281734.2",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1903C>A",
"hgvs_p": "p.Arg635Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001268663.1",
"strand": false,
"transcript": "NM_001281734.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 758,
"aa_ref": "R",
"aa_start": 630,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4323,
"cdna_start": 2503,
"cds_end": null,
"cds_length": 2277,
"cds_start": 1888,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000864217.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1888C>A",
"hgvs_p": "p.Arg630Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534276.1",
"strand": false,
"transcript": "ENST00000864217.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 708,
"aa_ref": "R",
"aa_start": 580,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4173,
"cdna_start": 2353,
"cds_end": null,
"cds_length": 2127,
"cds_start": 1738,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000864216.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.1738C>A",
"hgvs_p": "p.Arg580Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534275.1",
"strand": false,
"transcript": "ENST00000864216.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 362,
"aa_ref": "R",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2628,
"cdna_start": 802,
"cds_end": null,
"cds_length": 1089,
"cds_start": 700,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001281735.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.700C>A",
"hgvs_p": "p.Arg234Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001268664.1",
"strand": false,
"transcript": "NM_001281735.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 362,
"aa_ref": "R",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2633,
"cdna_start": 807,
"cds_end": null,
"cds_length": 1089,
"cds_start": 700,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_178441.2",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.700C>A",
"hgvs_p": "p.Arg234Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_848535.1",
"strand": false,
"transcript": "NM_178441.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 362,
"aa_ref": "R",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1183,
"cdna_start": 790,
"cds_end": null,
"cds_length": 1089,
"cds_start": 700,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000394207.6",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.700C>A",
"hgvs_p": "p.Arg234Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000377757.2",
"strand": false,
"transcript": "ENST00000394207.6",
"transcript_support_level": 2
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 362,
"aa_ref": "R",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3164,
"cdna_start": 1338,
"cds_end": null,
"cds_length": 1089,
"cds_start": 700,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_017021373.2",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.700C>A",
"hgvs_p": "p.Arg234Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016876862.1",
"strand": false,
"transcript": "XM_017021373.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 362,
"aa_ref": "R",
"aa_start": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3303,
"cdna_start": 1477,
"cds_end": null,
"cds_length": 1089,
"cds_start": 700,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047431482.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "c.700C>A",
"hgvs_p": "p.Arg234Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047287438.1",
"strand": false,
"transcript": "XM_047431482.1",
"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": 871,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000556040.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "n.530C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000556040.1",
"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": 545,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000556761.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "n.387C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000556761.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 556,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000554145.1",
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"hgvs_c": "n.*7C>A",
"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": "ENST00000554145.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs757263132",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0000013701671,
"gene_hgnc_id": 13180,
"gene_symbol": "ZFYVE1",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000137017,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.66,
"pos": 72974821,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_021260.4"
}
]
}