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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: 3-4362224-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=4362224&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 4362224,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000272902.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.1045C>T",
"hgvs_p": "p.Arg349Trp",
"transcript": "NM_182760.4",
"protein_id": "NP_877437.2",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 374,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 1069,
"cdna_end": null,
"cdna_length": 2147,
"mane_select": "ENST00000272902.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.1045C>T",
"hgvs_p": "p.Arg349Trp",
"transcript": "ENST00000272902.10",
"protein_id": "ENSP00000272902.5",
"transcript_support_level": 1,
"aa_start": 349,
"aa_end": null,
"aa_length": 374,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 1069,
"cdna_end": null,
"cdna_length": 2147,
"mane_select": "NM_182760.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.985C>T",
"hgvs_p": "p.Arg329Trp",
"transcript": "ENST00000405420.2",
"protein_id": "ENSP00000384977.2",
"transcript_support_level": 1,
"aa_start": 329,
"aa_end": null,
"aa_length": 354,
"cds_start": 985,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 1013,
"cdna_end": null,
"cdna_length": 1128,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.985C>T",
"hgvs_p": "p.Arg329Trp",
"transcript": "NM_001164675.2",
"protein_id": "NP_001158147.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 354,
"cds_start": 985,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 1009,
"cdna_end": null,
"cdna_length": 2087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.970C>T",
"hgvs_p": "p.Arg324Trp",
"transcript": "NM_001164674.2",
"protein_id": "NP_001158146.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 349,
"cds_start": 970,
"cds_end": null,
"cds_length": 1050,
"cdna_start": 994,
"cdna_end": null,
"cdna_length": 2072,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.970C>T",
"hgvs_p": "p.Arg324Trp",
"transcript": "ENST00000383843.9",
"protein_id": "ENSP00000373355.5",
"transcript_support_level": 2,
"aa_start": 324,
"aa_end": null,
"aa_length": 349,
"cds_start": 970,
"cds_end": null,
"cds_length": 1050,
"cdna_start": 989,
"cdna_end": null,
"cdna_length": 1447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.649C>T",
"hgvs_p": "p.Arg217Trp",
"transcript": "ENST00000458465.6",
"protein_id": "ENSP00000410060.2",
"transcript_support_level": 2,
"aa_start": 217,
"aa_end": null,
"aa_length": 242,
"cds_start": 649,
"cds_end": null,
"cds_length": 729,
"cdna_start": 673,
"cdna_end": null,
"cdna_length": 1102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.910C>T",
"hgvs_p": "p.Arg304Trp",
"transcript": "XM_047448025.1",
"protein_id": "XP_047303981.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 329,
"cds_start": 910,
"cds_end": null,
"cds_length": 990,
"cdna_start": 934,
"cdna_end": null,
"cdna_length": 2012,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "n.1014+14106C>T",
"hgvs_p": null,
"transcript": "ENST00000448413.5",
"protein_id": "ENSP00000404384.1",
"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": 3150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.1014+14106C>T",
"hgvs_p": null,
"transcript": "XM_011533624.4",
"protein_id": "XP_011531926.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 448,
"cds_start": -4,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.954+48641C>T",
"hgvs_p": null,
"transcript": "XM_017006252.3",
"protein_id": "XP_016861741.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 428,
"cds_start": -4,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5389,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.939+14106C>T",
"hgvs_p": null,
"transcript": "XM_017006253.2",
"protein_id": "XP_016861742.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 423,
"cds_start": -4,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.1014+14106C>T",
"hgvs_p": null,
"transcript": "XM_017006254.3",
"protein_id": "XP_016861743.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 402,
"cds_start": -4,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.1014+14106C>T",
"hgvs_p": null,
"transcript": "XM_011533625.4",
"protein_id": "XP_011531927.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 378,
"cds_start": -4,
"cds_end": null,
"cds_length": 1137,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.1015-10593C>T",
"hgvs_p": null,
"transcript": "XM_011533626.4",
"protein_id": "XP_011531928.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 372,
"cds_start": -4,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "c.939+14106C>T",
"hgvs_p": null,
"transcript": "XM_047448024.1",
"protein_id": "XP_047303980.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 353,
"cds_start": -4,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3437,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"hgvs_c": "n.1038+14106C>T",
"hgvs_p": null,
"transcript": "XR_007095664.1",
"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": 17732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SUMF1",
"gene_hgnc_id": 20376,
"dbsnp": "rs137852846",
"frequency_reference_population": 0.000004336906,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000410441,
"gnomad_genomes_af": 0.00000656978,
"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": 0.9883875846862793,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.808,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9648,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.56,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.912,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000272902.10",
"gene_symbol": "SUMF1",
"hgnc_id": 20376,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1045C>T",
"hgvs_p": "p.Arg349Trp"
}
],
"clinvar_disease": "Multiple sulfatase deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:1 O:1",
"phenotype_combined": "Multiple sulfatase deficiency|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}