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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: 17-40016314-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=40016314&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 40016314,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000759.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.277A>G",
"hgvs_p": "p.Ser93Gly",
"transcript": "NM_172219.3",
"protein_id": "NP_757373.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 204,
"cds_start": 277,
"cds_end": null,
"cds_length": 615,
"cdna_start": 312,
"cdna_end": null,
"cdna_length": 1504,
"mane_select": "ENST00000394149.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172219.3"
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.277A>G",
"hgvs_p": "p.Ser93Gly",
"transcript": "ENST00000394149.8",
"protein_id": "ENSP00000377705.4",
"transcript_support_level": 1,
"aa_start": 93,
"aa_end": null,
"aa_length": 204,
"cds_start": 277,
"cds_end": null,
"cds_length": 615,
"cdna_start": 312,
"cdna_end": null,
"cdna_length": 1504,
"mane_select": "NM_172219.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394149.8"
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.286A>G",
"hgvs_p": "p.Ser96Gly",
"transcript": "ENST00000225474.6",
"protein_id": "ENSP00000225474.2",
"transcript_support_level": 1,
"aa_start": 96,
"aa_end": null,
"aa_length": 207,
"cds_start": 286,
"cds_end": null,
"cds_length": 624,
"cdna_start": 317,
"cdna_end": null,
"cdna_length": 1509,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000225474.6"
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.265A>G",
"hgvs_p": "p.Ser89Gly",
"transcript": "ENST00000331769.6",
"protein_id": "ENSP00000327766.2",
"transcript_support_level": 1,
"aa_start": 89,
"aa_end": null,
"aa_length": 200,
"cds_start": 265,
"cds_end": null,
"cds_length": 603,
"cdna_start": 481,
"cdna_end": null,
"cdna_length": 1673,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000331769.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.184-171A>G",
"hgvs_p": null,
"transcript": "ENST00000577675.1",
"protein_id": "ENSP00000462991.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 164,
"cds_start": null,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1360,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000577675.1"
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.286A>G",
"hgvs_p": "p.Ser96Gly",
"transcript": "NM_000759.4",
"protein_id": "NP_000750.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 207,
"cds_start": 286,
"cds_end": null,
"cds_length": 624,
"cdna_start": 321,
"cdna_end": null,
"cdna_length": 1513,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000759.4"
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.277A>G",
"hgvs_p": "p.Ser93Gly",
"transcript": "ENST00000945857.1",
"protein_id": "ENSP00000615916.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 189,
"cds_start": 277,
"cds_end": null,
"cds_length": 570,
"cdna_start": 391,
"cdna_end": null,
"cdna_length": 1541,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945857.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.205-171A>G",
"hgvs_p": null,
"transcript": "NM_172220.3",
"protein_id": "NP_757374.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 171,
"cds_start": null,
"cds_end": null,
"cds_length": 516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1405,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172220.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.205-171A>G",
"hgvs_p": null,
"transcript": "ENST00000394148.7",
"protein_id": "ENSP00000377704.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 171,
"cds_start": null,
"cds_end": null,
"cds_length": 516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 622,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394148.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.196-171A>G",
"hgvs_p": null,
"transcript": "NM_001178147.2",
"protein_id": "NP_001171618.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1396,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001178147.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "c.196-171A>G",
"hgvs_p": null,
"transcript": "ENST00000583218.5",
"protein_id": "ENSP00000464421.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 154,
"cds_start": null,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 579,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000583218.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "n.481A>G",
"hgvs_p": null,
"transcript": "ENST00000479880.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 947,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000479880.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "n.122A>G",
"hgvs_p": null,
"transcript": "ENST00000579852.1",
"protein_id": "ENSP00000464157.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1288,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000579852.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "n.488A>G",
"hgvs_p": null,
"transcript": "NR_033662.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1680,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033662.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "n.497A>G",
"hgvs_p": null,
"transcript": "NR_168491.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1689,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_168491.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "n.407-171A>G",
"hgvs_p": null,
"transcript": "NR_168489.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1572,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_168489.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "n.416-171A>G",
"hgvs_p": null,
"transcript": "NR_168490.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1581,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_168490.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"hgvs_c": "n.*152A>G",
"hgvs_p": null,
"transcript": "ENST00000582798.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 552,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000582798.1"
}
],
"gene_symbol": "CSF3",
"gene_hgnc_id": 2438,
"dbsnp": "rs749012642",
"frequency_reference_population": 0.00013719329,
"hom_count_reference_population": 0,
"allele_count_reference_population": 221,
"gnomad_exomes_af": 0.000145318,
"gnomad_genomes_af": 0.0000592113,
"gnomad_exomes_ac": 212,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.24360701441764832,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.023,
"revel_prediction": "Benign",
"alphamissense_score": 0.0688,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.003,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_000759.4",
"gene_symbol": "CSF3",
"hgnc_id": 2438,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.286A>G",
"hgvs_p": "p.Ser96Gly"
}
],
"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
}