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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: 3-58192729-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=58192729&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 58192729,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_004944.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.876A>G",
"hgvs_p": "p.Lys292Lys",
"transcript": "NM_004944.4",
"protein_id": "NP_004935.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 305,
"cds_start": 876,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000394549.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004944.4"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.876A>G",
"hgvs_p": "p.Lys292Lys",
"transcript": "ENST00000394549.7",
"protein_id": "ENSP00000378053.2",
"transcript_support_level": 1,
"aa_start": 292,
"aa_end": null,
"aa_length": 305,
"cds_start": 876,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004944.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394549.7"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.401A>G",
"hgvs_p": "p.Asn134Ser",
"transcript": "ENST00000477209.5",
"protein_id": "ENSP00000417976.1",
"transcript_support_level": 2,
"aa_start": 134,
"aa_end": null,
"aa_length": 137,
"cds_start": 401,
"cds_end": null,
"cds_length": 414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000477209.5"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.903A>G",
"hgvs_p": "p.Lys301Lys",
"transcript": "ENST00000907344.1",
"protein_id": "ENSP00000577403.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 314,
"cds_start": 903,
"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": "ENST00000907344.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.897A>G",
"hgvs_p": "p.Lys299Lys",
"transcript": "ENST00000907342.1",
"protein_id": "ENSP00000577401.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 312,
"cds_start": 897,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907342.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.876A>G",
"hgvs_p": "p.Lys292Lys",
"transcript": "ENST00000907339.1",
"protein_id": "ENSP00000577398.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 305,
"cds_start": 876,
"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": "ENST00000907339.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.876A>G",
"hgvs_p": "p.Lys292Lys",
"transcript": "ENST00000907340.1",
"protein_id": "ENSP00000577399.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 305,
"cds_start": 876,
"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": "ENST00000907340.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.867A>G",
"hgvs_p": "p.Lys289Lys",
"transcript": "ENST00000907341.1",
"protein_id": "ENSP00000577400.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 302,
"cds_start": 867,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907341.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.837A>G",
"hgvs_p": "p.Lys279Lys",
"transcript": "ENST00000907343.1",
"protein_id": "ENSP00000577402.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 292,
"cds_start": 837,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907343.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.786A>G",
"hgvs_p": "p.Lys262Lys",
"transcript": "NM_001256560.2",
"protein_id": "NP_001243489.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 275,
"cds_start": 786,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001256560.2"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.786A>G",
"hgvs_p": "p.Lys262Lys",
"transcript": "ENST00000486455.5",
"protein_id": "ENSP00000419052.1",
"transcript_support_level": 2,
"aa_start": 262,
"aa_end": null,
"aa_length": 275,
"cds_start": 786,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000486455.5"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.786A>G",
"hgvs_p": "p.Lys262Lys",
"transcript": "ENST00000907338.1",
"protein_id": "ENSP00000577397.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 275,
"cds_start": 786,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907338.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"hgvs_c": "c.*548A>G",
"hgvs_p": null,
"transcript": "ENST00000483681.5",
"protein_id": "ENSP00000417047.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": null,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000483681.5"
}
],
"gene_symbol": "DNASE1L3",
"gene_hgnc_id": 2959,
"dbsnp": "rs774817141",
"frequency_reference_population": 6.840947e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84095e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12263372540473938,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.03,
"revel_prediction": "Benign",
"alphamissense_score": 0.0945,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.89,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP7",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_004944.4",
"gene_symbol": "DNASE1L3",
"hgnc_id": 2959,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.876A>G",
"hgvs_p": "p.Lys292Lys"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}