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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: 5-78885826-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=78885826&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 78885826,
"ref": "A",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_000046.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "NM_000046.5",
"protein_id": "NP_000037.2",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 533,
"cds_start": 900,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 4852,
"mane_select": "ENST00000264914.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "ENST00000264914.10",
"protein_id": "ENSP00000264914.4",
"transcript_support_level": 1,
"aa_start": 300,
"aa_end": null,
"aa_length": 533,
"cds_start": 900,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 4852,
"mane_select": "NM_000046.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "ENST00000396151.7",
"protein_id": "ENSP00000379455.3",
"transcript_support_level": 1,
"aa_start": 300,
"aa_end": null,
"aa_length": 413,
"cds_start": 900,
"cds_end": null,
"cds_length": 1242,
"cdna_start": 1399,
"cdna_end": null,
"cdna_length": 2316,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "ENST00000565165.2",
"protein_id": "ENSP00000456339.2",
"transcript_support_level": 1,
"aa_start": 300,
"aa_end": null,
"aa_length": 398,
"cds_start": 900,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 901,
"cdna_end": null,
"cdna_length": 3845,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "NM_198709.3",
"protein_id": "NP_942002.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 413,
"cds_start": 900,
"cds_end": null,
"cds_length": 1242,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 2187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "XM_011543390.2",
"protein_id": "XP_011541692.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 533,
"cds_start": 900,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 5160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "XM_017009471.3",
"protein_id": "XP_016864960.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 451,
"cds_start": 900,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 4026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "XM_011543391.4",
"protein_id": "XP_011541693.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 442,
"cds_start": 900,
"cds_end": null,
"cds_length": 1329,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 1402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "XM_011543392.4",
"protein_id": "XP_011541694.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 405,
"cds_start": 900,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 1499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu",
"transcript": "XM_011543393.3",
"protein_id": "XP_011541695.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 382,
"cds_start": 900,
"cds_end": null,
"cds_length": 1149,
"cdna_start": 962,
"cdna_end": null,
"cdna_length": 2034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "n.82T>A",
"hgvs_p": null,
"transcript": "ENST00000521800.2",
"protein_id": null,
"transcript_support_level": 2,
"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": 1159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "n.962T>A",
"hgvs_p": null,
"transcript": "XR_001742065.3",
"protein_id": null,
"transcript_support_level": null,
"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": 2491,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"hgvs_c": "n.962T>A",
"hgvs_p": null,
"transcript": "XR_001742066.3",
"protein_id": null,
"transcript_support_level": null,
"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": 1518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ARSB",
"gene_hgnc_id": 714,
"dbsnp": "rs1280123243",
"frequency_reference_population": 0.000004336825,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000410427,
"gnomad_genomes_af": 0.00000657065,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.993085503578186,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.21199999749660492,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.943,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9929,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.53,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.62,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000277829308136108,
"dbscsnv_ada_prediction": "Benign",
"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": "NM_000046.5",
"gene_symbol": "ARSB",
"hgnc_id": 714,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.900T>A",
"hgvs_p": "p.Asp300Glu"
}
],
"clinvar_disease": "Mucopolysaccharidosis type 6,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:1",
"phenotype_combined": "Mucopolysaccharidosis type 6|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}