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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: 12-44520109-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=44520109&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 44520109,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001145107.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Cys",
"transcript": "NM_001145108.2",
"protein_id": "NP_001138580.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 816,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2742,
"cdna_end": null,
"cdna_length": 3553,
"mane_select": "ENST00000429094.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145108.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Cys",
"transcript": "ENST00000429094.7",
"protein_id": "ENSP00000390680.2",
"transcript_support_level": 1,
"aa_start": 766,
"aa_end": null,
"aa_length": 816,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2742,
"cdna_end": null,
"cdna_length": 3553,
"mane_select": "NM_001145108.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000429094.7"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Cys",
"transcript": "ENST00000452445.6",
"protein_id": "ENSP00000394612.2",
"transcript_support_level": 1,
"aa_start": 766,
"aa_end": null,
"aa_length": 816,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2389,
"cdna_end": null,
"cdna_length": 3196,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452445.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2293C>T",
"hgvs_p": "p.Arg765Cys",
"transcript": "ENST00000395487.6",
"protein_id": "ENSP00000378866.2",
"transcript_support_level": 1,
"aa_start": 765,
"aa_end": null,
"aa_length": 815,
"cds_start": 2293,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 2389,
"cdna_end": null,
"cdna_length": 3203,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395487.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2152C>T",
"hgvs_p": "p.Arg718Cys",
"transcript": "ENST00000551601.5",
"protein_id": "ENSP00000449332.1",
"transcript_support_level": 1,
"aa_start": 718,
"aa_end": null,
"aa_length": 768,
"cds_start": 2152,
"cds_end": null,
"cds_length": 2307,
"cdna_start": 2341,
"cdna_end": null,
"cdna_length": 3148,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000551601.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2446C>T",
"hgvs_p": "p.Arg816Cys",
"transcript": "NM_001145107.2",
"protein_id": "NP_001138579.1",
"transcript_support_level": null,
"aa_start": 816,
"aa_end": null,
"aa_length": 866,
"cds_start": 2446,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2596,
"cdna_end": null,
"cdna_length": 3407,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145107.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2446C>T",
"hgvs_p": "p.Arg816Cys",
"transcript": "ENST00000437801.6",
"protein_id": "ENSP00000416341.2",
"transcript_support_level": 2,
"aa_start": 816,
"aa_end": null,
"aa_length": 866,
"cds_start": 2446,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2818,
"cdna_end": null,
"cdna_length": 3279,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000437801.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Arg789Cys",
"transcript": "NM_001145110.2",
"protein_id": "NP_001138582.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 839,
"cds_start": 2365,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 2518,
"cdna_end": null,
"cdna_length": 3329,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145110.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Arg789Cys",
"transcript": "ENST00000333837.8",
"protein_id": "ENSP00000327988.4",
"transcript_support_level": 2,
"aa_start": 789,
"aa_end": null,
"aa_length": 839,
"cds_start": 2365,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 2457,
"cdna_end": null,
"cdna_length": 2943,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000333837.8"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Cys",
"transcript": "NM_006159.2",
"protein_id": "NP_006150.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 816,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2498,
"cdna_end": null,
"cdna_length": 3312,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006159.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Cys",
"transcript": "ENST00000868481.1",
"protein_id": "ENSP00000538540.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 816,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2510,
"cdna_end": null,
"cdna_length": 3319,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868481.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Cys",
"transcript": "ENST00000967237.1",
"protein_id": "ENSP00000637296.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 816,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2488,
"cdna_end": null,
"cdna_length": 3302,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967237.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2293C>T",
"hgvs_p": "p.Arg765Cys",
"transcript": "NM_001145109.2",
"protein_id": "NP_001138581.1",
"transcript_support_level": null,
"aa_start": 765,
"aa_end": null,
"aa_length": 815,
"cds_start": 2293,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 2351,
"cdna_end": null,
"cdna_length": 3162,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145109.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2293C>T",
"hgvs_p": "p.Arg765Cys",
"transcript": "ENST00000549027.5",
"protein_id": "ENSP00000447927.1",
"transcript_support_level": 5,
"aa_start": 765,
"aa_end": null,
"aa_length": 815,
"cds_start": 2293,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 2482,
"cdna_end": null,
"cdna_length": 3036,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000549027.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2155C>T",
"hgvs_p": "p.Arg719Cys",
"transcript": "ENST00000967238.1",
"protein_id": "ENSP00000637297.1",
"transcript_support_level": null,
"aa_start": 719,
"aa_end": null,
"aa_length": 769,
"cds_start": 2155,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 2374,
"cdna_end": null,
"cdna_length": 3181,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967238.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2056C>T",
"hgvs_p": "p.Arg686Cys",
"transcript": "ENST00000868482.1",
"protein_id": "ENSP00000538541.1",
"transcript_support_level": null,
"aa_start": 686,
"aa_end": null,
"aa_length": 736,
"cds_start": 2056,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 2502,
"cdna_end": null,
"cdna_length": 3317,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868482.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1972C>T",
"hgvs_p": "p.Arg658Cys",
"transcript": "ENST00000967239.1",
"protein_id": "ENSP00000637298.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 708,
"cds_start": 1972,
"cds_end": null,
"cds_length": 2127,
"cdna_start": 2153,
"cdna_end": null,
"cdna_length": 2960,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967239.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2296C>T",
"hgvs_p": "p.Arg766Cys",
"transcript": "XM_011538396.2",
"protein_id": "XP_011536698.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 816,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2447,
"cdna_end": null,
"cdna_length": 3261,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538396.2"
}
],
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"dbsnp": "rs375958961",
"frequency_reference_population": 0.00010532707,
"hom_count_reference_population": 1,
"allele_count_reference_population": 170,
"gnomad_exomes_af": 0.00010124,
"gnomad_genomes_af": 0.000144602,
"gnomad_exomes_ac": 148,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.37782368063926697,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.531,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2561,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.769,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "NM_001145107.2",
"gene_symbol": "NELL2",
"hgnc_id": 7751,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2446C>T",
"hgvs_p": "p.Arg816Cys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}