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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: 18-23535657-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=23535657&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 23535657,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000269228.10",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Asp1097Asn",
"transcript": "NM_000271.5",
"protein_id": "NP_000262.2",
"transcript_support_level": null,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1278,
"cds_start": 3289,
"cds_end": null,
"cds_length": 3837,
"cdna_start": 3452,
"cdna_end": null,
"cdna_length": 4760,
"mane_select": "ENST00000269228.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Asp1097Asn",
"transcript": "ENST00000269228.10",
"protein_id": "ENSP00000269228.4",
"transcript_support_level": 1,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1278,
"cds_start": 3289,
"cds_end": null,
"cds_length": 3837,
"cdna_start": 3452,
"cdna_end": null,
"cdna_length": 4760,
"mane_select": "NM_000271.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"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": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.2365G>A",
"hgvs_p": "p.Asp789Asn",
"transcript": "ENST00000591051.1",
"protein_id": "ENSP00000467636.1",
"transcript_support_level": 2,
"aa_start": 789,
"aa_end": null,
"aa_length": 970,
"cds_start": 2365,
"cds_end": null,
"cds_length": 2913,
"cdna_start": 2367,
"cdna_end": null,
"cdna_length": 3171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.43G>A",
"hgvs_p": "p.Asp15Asn",
"transcript": "ENST00000586150.5",
"protein_id": "ENSP00000468321.1",
"transcript_support_level": 3,
"aa_start": 15,
"aa_end": null,
"aa_length": 174,
"cds_start": 43,
"cds_end": null,
"cds_length": 525,
"cdna_start": 44,
"cdna_end": null,
"cdna_length": 571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3340G>A",
"hgvs_p": "p.Asp1114Asn",
"transcript": "XM_005258277.1",
"protein_id": "XP_005258334.1",
"transcript_support_level": null,
"aa_start": 1114,
"aa_end": null,
"aa_length": 1303,
"cds_start": 3340,
"cds_end": null,
"cds_length": 3912,
"cdna_start": 3503,
"cdna_end": null,
"cdna_length": 4427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3340G>A",
"hgvs_p": "p.Asp1114Asn",
"transcript": "XM_005258278.6",
"protein_id": "XP_005258335.1",
"transcript_support_level": null,
"aa_start": 1114,
"aa_end": null,
"aa_length": 1295,
"cds_start": 3340,
"cds_end": null,
"cds_length": 3888,
"cdna_start": 3503,
"cdna_end": null,
"cdna_length": 4811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Asp1097Asn",
"transcript": "XM_005258279.3",
"protein_id": "XP_005258336.1",
"transcript_support_level": null,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1286,
"cds_start": 3289,
"cds_end": null,
"cds_length": 3861,
"cdna_start": 3452,
"cdna_end": null,
"cdna_length": 4376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3340G>A",
"hgvs_p": "p.Asp1114Asn",
"transcript": "XM_017025784.1",
"protein_id": "XP_016881273.1",
"transcript_support_level": null,
"aa_start": 1114,
"aa_end": null,
"aa_length": 1281,
"cds_start": 3340,
"cds_end": null,
"cds_length": 3846,
"cdna_start": 3503,
"cdna_end": null,
"cdna_length": 5489,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3340G>A",
"hgvs_p": "p.Asp1114Asn",
"transcript": "XM_006722479.4",
"protein_id": "XP_006722542.1",
"transcript_support_level": null,
"aa_start": 1114,
"aa_end": null,
"aa_length": 1273,
"cds_start": 3340,
"cds_end": null,
"cds_length": 3822,
"cdna_start": 3503,
"cdna_end": null,
"cdna_length": 5284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3340G>A",
"hgvs_p": "p.Asp1114Asn",
"transcript": "XM_017025785.1",
"protein_id": "XP_016881274.1",
"transcript_support_level": null,
"aa_start": 1114,
"aa_end": null,
"aa_length": 1273,
"cds_start": 3340,
"cds_end": null,
"cds_length": 3822,
"cdna_start": 3503,
"cdna_end": null,
"cdna_length": 5116,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Asp1097Asn",
"transcript": "XM_017025786.2",
"protein_id": "XP_016881275.1",
"transcript_support_level": null,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1264,
"cds_start": 3289,
"cds_end": null,
"cds_length": 3795,
"cdna_start": 3452,
"cdna_end": null,
"cdna_length": 5438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Asp1097Asn",
"transcript": "XM_017025787.2",
"protein_id": "XP_016881276.1",
"transcript_support_level": null,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1256,
"cds_start": 3289,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 3452,
"cdna_end": null,
"cdna_length": 5233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Asp1097Asn",
"transcript": "XM_047437539.1",
"protein_id": "XP_047293495.1",
"transcript_support_level": null,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1256,
"cds_start": 3289,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 3452,
"cdna_end": null,
"cdna_length": 5065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "n.44G>A",
"hgvs_p": null,
"transcript": "ENST00000588867.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"hgvs_c": "c.-36G>A",
"hgvs_p": null,
"transcript": "ENST00000591107.6",
"protein_id": "ENSP00000468438.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 178,
"cds_start": -4,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPC1",
"gene_hgnc_id": 7897,
"dbsnp": "rs758829443",
"frequency_reference_population": 0.000011153107,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000102609,
"gnomad_genomes_af": 0.0000197314,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9747660160064697,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.564,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1364,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.9,
"phylop100way_prediction": "Pathogenic",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000269228.10",
"gene_symbol": "NPC1",
"hgnc_id": 7897,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Asp1097Asn"
}
],
"clinvar_disease": " type C1,Niemann-Pick disease,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:1",
"phenotype_combined": "not provided|Niemann-Pick disease, type C1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}