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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: 19-47475477-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=47475477&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KPTN",
"hgnc_id": 6404,
"hgvs_c": "c.1250G>A",
"hgvs_p": "p.Arg417His",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_007059.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000287896",
"hgnc_id": null,
"hgvs_c": "n.69-985C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000669287.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 37,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0785,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases,Macrocephaly-developmental delay syndrome",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.03634589910507202,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1636,
"cdna_start": 1309,
"cds_end": null,
"cds_length": 1311,
"cds_start": 1250,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_007059.4",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1250G>A",
"hgvs_p": "p.Arg417His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000338134.8",
"protein_coding": true,
"protein_id": "NP_008990.2",
"strand": false,
"transcript": "NM_007059.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1636,
"cdna_start": 1309,
"cds_end": null,
"cds_length": 1311,
"cds_start": 1250,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000338134.8",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1250G>A",
"hgvs_p": "p.Arg417His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007059.4",
"protein_coding": true,
"protein_id": "ENSP00000337850.2",
"strand": false,
"transcript": "ENST00000338134.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 474,
"aa_ref": "R",
"aa_start": 455,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1792,
"cdna_start": 1456,
"cds_end": null,
"cds_length": 1425,
"cds_start": 1364,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000914957.1",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1364G>A",
"hgvs_p": "p.Arg455His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585016.1",
"strand": false,
"transcript": "ENST00000914957.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 417,
"aa_ref": "R",
"aa_start": 398,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1547,
"cdna_start": 1222,
"cds_end": null,
"cds_length": 1254,
"cds_start": 1193,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000968682.1",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1193G>A",
"hgvs_p": "p.Arg398His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638741.1",
"strand": false,
"transcript": "ENST00000968682.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 401,
"aa_ref": "R",
"aa_start": 382,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1543,
"cdna_start": 1216,
"cds_end": null,
"cds_length": 1206,
"cds_start": 1145,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000914958.1",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1145G>A",
"hgvs_p": "p.Arg382His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000585017.1",
"strand": false,
"transcript": "ENST00000914958.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 380,
"aa_ref": "R",
"aa_start": 361,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1468,
"cdna_start": 1141,
"cds_end": null,
"cds_length": 1143,
"cds_start": 1082,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001291296.2",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1082G>A",
"hgvs_p": "p.Arg361His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278225.1",
"strand": false,
"transcript": "NM_001291296.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 559,
"aa_ref": "R",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1946,
"cdna_start": 1619,
"cds_end": null,
"cds_length": 1680,
"cds_start": 1619,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_017026227.2",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016881716.1",
"strand": false,
"transcript": "XM_017026227.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 520,
"aa_ref": "R",
"aa_start": 501,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1829,
"cdna_start": 1502,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1502,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_017026228.2",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1502G>A",
"hgvs_p": "p.Arg501His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016881717.1",
"strand": false,
"transcript": "XM_017026228.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 475,
"aa_ref": "R",
"aa_start": 456,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1753,
"cdna_start": 1426,
"cds_end": null,
"cds_length": 1428,
"cds_start": 1367,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_024451333.2",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "c.1367G>A",
"hgvs_p": "p.Arg456His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024307101.1",
"strand": false,
"transcript": "XM_024451333.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1623,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000594208.5",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "n.*884G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000470364.1",
"strand": false,
"transcript": "ENST00000594208.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 468,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000600551.1",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "n.141G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000600551.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1723,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NR_111923.2",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "n.1396G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_111923.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1623,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000594208.5",
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"hgvs_c": "n.*884G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000470364.1",
"strand": false,
"transcript": "ENST00000594208.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2157,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000669287.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000287896",
"hgvs_c": "n.69-985C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000669287.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1778,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000746654.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000287896",
"hgvs_c": "n.160-985C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000746654.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs372235519",
"effect": "missense_variant",
"frequency_reference_population": 0.000022932965,
"gene_hgnc_id": 6404,
"gene_symbol": "KPTN",
"gnomad_exomes_ac": 33,
"gnomad_exomes_af": 0.0000225846,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262771,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Macrocephaly-developmental delay syndrome|Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.185,
"pos": 47475477,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.063,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_007059.4"
}
]
}