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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: 9-137040408-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=137040408&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 137040408,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_015392.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.737C>T",
"hgvs_p": "p.Ala246Val",
"transcript": "NM_015392.4",
"protein_id": "NP_056207.3",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 325,
"cds_start": 737,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371601.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015392.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.737C>T",
"hgvs_p": "p.Ala246Val",
"transcript": "ENST00000371601.5",
"protein_id": "ENSP00000360660.4",
"transcript_support_level": 1,
"aa_start": 246,
"aa_end": null,
"aa_length": 325,
"cds_start": 737,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015392.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371601.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.971C>T",
"hgvs_p": "p.Ala324Val",
"transcript": "ENST00000371600.7",
"protein_id": "ENSP00000360659.3",
"transcript_support_level": 1,
"aa_start": 324,
"aa_end": null,
"aa_length": 403,
"cds_start": 971,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371600.7"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.739C>T",
"hgvs_p": "p.Arg247Trp",
"transcript": "ENST00000952624.1",
"protein_id": "ENSP00000622683.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 355,
"cds_start": 739,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952624.1"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.709C>T",
"hgvs_p": "p.Arg237Trp",
"transcript": "ENST00000872941.1",
"protein_id": "ENSP00000543000.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 345,
"cds_start": 709,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872941.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.737C>T",
"hgvs_p": "p.Ala246Val",
"transcript": "ENST00000872942.1",
"protein_id": "ENSP00000543001.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 337,
"cds_start": 737,
"cds_end": null,
"cds_length": 1014,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872942.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.767C>T",
"hgvs_p": "p.Ala256Val",
"transcript": "ENST00000952625.1",
"protein_id": "ENSP00000622684.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 335,
"cds_start": 767,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952625.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.731C>T",
"hgvs_p": "p.Ala244Val",
"transcript": "ENST00000872939.1",
"protein_id": "ENSP00000542998.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 323,
"cds_start": 731,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872939.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.731C>T",
"hgvs_p": "p.Ala244Val",
"transcript": "ENST00000872946.1",
"protein_id": "ENSP00000543005.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 323,
"cds_start": 731,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872946.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.704C>T",
"hgvs_p": "p.Ala235Val",
"transcript": "ENST00000872945.1",
"protein_id": "ENSP00000543004.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 314,
"cds_start": 704,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872945.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.677C>T",
"hgvs_p": "p.Ala226Val",
"transcript": "ENST00000872940.1",
"protein_id": "ENSP00000542999.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 305,
"cds_start": 677,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872940.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.566C>T",
"hgvs_p": "p.Ala189Val",
"transcript": "ENST00000872938.1",
"protein_id": "ENSP00000542997.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 268,
"cds_start": 566,
"cds_end": null,
"cds_length": 807,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872938.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.533C>T",
"hgvs_p": "p.Ala178Val",
"transcript": "ENST00000872944.1",
"protein_id": "ENSP00000543003.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 257,
"cds_start": 533,
"cds_end": null,
"cds_length": 774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872944.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.419C>T",
"hgvs_p": "p.Ala140Val",
"transcript": "ENST00000872943.1",
"protein_id": "ENSP00000543002.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 219,
"cds_start": 419,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872943.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "ENSG00000279073",
"gene_hgnc_id": null,
"hgvs_c": "c.28C>T",
"hgvs_p": "p.Arg10Trp",
"transcript": "ENST00000625047.3",
"protein_id": "ENSP00000485275.1",
"transcript_support_level": 3,
"aa_start": 10,
"aa_end": null,
"aa_length": 76,
"cds_start": 28,
"cds_end": null,
"cds_length": 231,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000625047.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000279073",
"gene_hgnc_id": null,
"hgvs_c": "c.-21C>T",
"hgvs_p": null,
"transcript": "ENST00000622933.1",
"protein_id": "ENSP00000485208.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 108,
"cds_start": null,
"cds_end": null,
"cds_length": 327,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000622933.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"hgvs_c": "c.-32C>T",
"hgvs_p": null,
"transcript": "ENST00000472668.1",
"protein_id": "ENSP00000481901.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 27,
"cds_start": null,
"cds_end": null,
"cds_length": 84,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000472668.1"
}
],
"gene_symbol": "NPDC1",
"gene_hgnc_id": 7899,
"dbsnp": "rs907643236",
"frequency_reference_population": 0.000015491967,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.000015747,
"gnomad_genomes_af": 0.0000131492,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8777114152908325,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.531,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5106,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.014,
"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": 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_015392.4",
"gene_symbol": "NPDC1",
"hgnc_id": 7899,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.737C>T",
"hgvs_p": "p.Ala246Val"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000625047.3",
"gene_symbol": "ENSG00000279073",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.28C>T",
"hgvs_p": "p.Arg10Trp"
}
],
"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
}