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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: 12-44523364-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=44523364&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 44523364,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001145107.2",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1925A>G",
"hgvs_p": "p.His642Arg",
"transcript": "NM_001145108.2",
"protein_id": "NP_001138580.1",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 816,
"cds_start": 1925,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2371,
"cdna_end": null,
"cdna_length": 3553,
"mane_select": "ENST00000429094.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145108.2"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1925A>G",
"hgvs_p": "p.His642Arg",
"transcript": "ENST00000429094.7",
"protein_id": "ENSP00000390680.2",
"transcript_support_level": 1,
"aa_start": 642,
"aa_end": null,
"aa_length": 816,
"cds_start": 1925,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2371,
"cdna_end": null,
"cdna_length": 3553,
"mane_select": "NM_001145108.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000429094.7"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1925A>G",
"hgvs_p": "p.His642Arg",
"transcript": "ENST00000452445.6",
"protein_id": "ENSP00000394612.2",
"transcript_support_level": 1,
"aa_start": 642,
"aa_end": null,
"aa_length": 816,
"cds_start": 1925,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2018,
"cdna_end": null,
"cdna_length": 3196,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452445.6"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1922A>G",
"hgvs_p": "p.His641Arg",
"transcript": "ENST00000395487.6",
"protein_id": "ENSP00000378866.2",
"transcript_support_level": 1,
"aa_start": 641,
"aa_end": null,
"aa_length": 815,
"cds_start": 1922,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 2018,
"cdna_end": null,
"cdna_length": 3203,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395487.6"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1781A>G",
"hgvs_p": "p.His594Arg",
"transcript": "ENST00000551601.5",
"protein_id": "ENSP00000449332.1",
"transcript_support_level": 1,
"aa_start": 594,
"aa_end": null,
"aa_length": 768,
"cds_start": 1781,
"cds_end": null,
"cds_length": 2307,
"cdna_start": 1970,
"cdna_end": null,
"cdna_length": 3148,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000551601.5"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2075A>G",
"hgvs_p": "p.His692Arg",
"transcript": "NM_001145107.2",
"protein_id": "NP_001138579.1",
"transcript_support_level": null,
"aa_start": 692,
"aa_end": null,
"aa_length": 866,
"cds_start": 2075,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2225,
"cdna_end": null,
"cdna_length": 3407,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145107.2"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.2075A>G",
"hgvs_p": "p.His692Arg",
"transcript": "ENST00000437801.6",
"protein_id": "ENSP00000416341.2",
"transcript_support_level": 2,
"aa_start": 692,
"aa_end": null,
"aa_length": 866,
"cds_start": 2075,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2447,
"cdna_end": null,
"cdna_length": 3279,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000437801.6"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1994A>G",
"hgvs_p": "p.His665Arg",
"transcript": "NM_001145110.2",
"protein_id": "NP_001138582.1",
"transcript_support_level": null,
"aa_start": 665,
"aa_end": null,
"aa_length": 839,
"cds_start": 1994,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 2147,
"cdna_end": null,
"cdna_length": 3329,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145110.2"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1994A>G",
"hgvs_p": "p.His665Arg",
"transcript": "ENST00000333837.8",
"protein_id": "ENSP00000327988.4",
"transcript_support_level": 2,
"aa_start": 665,
"aa_end": null,
"aa_length": 839,
"cds_start": 1994,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 2086,
"cdna_end": null,
"cdna_length": 2943,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000333837.8"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1925A>G",
"hgvs_p": "p.His642Arg",
"transcript": "NM_006159.2",
"protein_id": "NP_006150.1",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 816,
"cds_start": 1925,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2127,
"cdna_end": null,
"cdna_length": 3312,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006159.2"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1925A>G",
"hgvs_p": "p.His642Arg",
"transcript": "ENST00000868481.1",
"protein_id": "ENSP00000538540.1",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 816,
"cds_start": 1925,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2139,
"cdna_end": null,
"cdna_length": 3319,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868481.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1925A>G",
"hgvs_p": "p.His642Arg",
"transcript": "ENST00000967237.1",
"protein_id": "ENSP00000637296.1",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 816,
"cds_start": 1925,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2117,
"cdna_end": null,
"cdna_length": 3302,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967237.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1922A>G",
"hgvs_p": "p.His641Arg",
"transcript": "NM_001145109.2",
"protein_id": "NP_001138581.1",
"transcript_support_level": null,
"aa_start": 641,
"aa_end": null,
"aa_length": 815,
"cds_start": 1922,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 1980,
"cdna_end": null,
"cdna_length": 3162,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145109.2"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1922A>G",
"hgvs_p": "p.His641Arg",
"transcript": "ENST00000549027.5",
"protein_id": "ENSP00000447927.1",
"transcript_support_level": 5,
"aa_start": 641,
"aa_end": null,
"aa_length": 815,
"cds_start": 1922,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 2111,
"cdna_end": null,
"cdna_length": 3036,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000549027.5"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1784A>G",
"hgvs_p": "p.His595Arg",
"transcript": "ENST00000967238.1",
"protein_id": "ENSP00000637297.1",
"transcript_support_level": null,
"aa_start": 595,
"aa_end": null,
"aa_length": 769,
"cds_start": 1784,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 2003,
"cdna_end": null,
"cdna_length": 3181,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967238.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1925A>G",
"hgvs_p": "p.His642Arg",
"transcript": "ENST00000868482.1",
"protein_id": "ENSP00000538541.1",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 736,
"cds_start": 1925,
"cds_end": null,
"cds_length": 2211,
"cdna_start": 2371,
"cdna_end": null,
"cdna_length": 3317,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868482.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1601A>G",
"hgvs_p": "p.His534Arg",
"transcript": "ENST00000967239.1",
"protein_id": "ENSP00000637298.1",
"transcript_support_level": null,
"aa_start": 534,
"aa_end": null,
"aa_length": 708,
"cds_start": 1601,
"cds_end": null,
"cds_length": 2127,
"cdna_start": 1782,
"cdna_end": null,
"cdna_length": 2960,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967239.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.161A>G",
"hgvs_p": "p.His54Arg",
"transcript": "ENST00000550139.1",
"protein_id": "ENSP00000448107.1",
"transcript_support_level": 3,
"aa_start": 54,
"aa_end": null,
"aa_length": 85,
"cds_start": 161,
"cds_end": null,
"cds_length": 258,
"cdna_start": 162,
"cdna_end": null,
"cdna_length": 749,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000550139.1"
},
{
"aa_ref": "H",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "c.1925A>G",
"hgvs_p": "p.His642Arg",
"transcript": "XM_011538396.2",
"protein_id": "XP_011536698.1",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 816,
"cds_start": 1925,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2076,
"cdna_end": null,
"cdna_length": 3261,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538396.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"hgvs_c": "n.272A>G",
"hgvs_p": null,
"transcript": "ENST00000547636.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 560,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000547636.1"
}
],
"gene_symbol": "NELL2",
"gene_hgnc_id": 7751,
"dbsnp": "rs773598023",
"frequency_reference_population": 6.8405257e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84053e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.85505610704422,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.835,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1537,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.36,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.01,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001145107.2",
"gene_symbol": "NELL2",
"hgnc_id": 7751,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2075A>G",
"hgvs_p": "p.His692Arg"
}
],
"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
}