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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: 4-94640308-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=94640308&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 94640308,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000317968.9",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.1141A>G",
"hgvs_p": "p.Thr381Ala",
"transcript": "NM_006457.5",
"protein_id": "NP_006448.5",
"transcript_support_level": null,
"aa_start": 381,
"aa_end": null,
"aa_length": 596,
"cds_start": 1141,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 1237,
"cdna_end": null,
"cdna_length": 6043,
"mane_select": "ENST00000317968.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.1141A>G",
"hgvs_p": "p.Thr381Ala",
"transcript": "ENST00000317968.9",
"protein_id": "ENSP00000321746.4",
"transcript_support_level": 1,
"aa_start": 381,
"aa_end": null,
"aa_length": 596,
"cds_start": 1141,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 1237,
"cdna_end": null,
"cdna_length": 6043,
"mane_select": "NM_006457.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.1228A>G",
"hgvs_p": "p.Thr410Ala",
"transcript": "ENST00000615540.4",
"protein_id": "ENSP00000480359.1",
"transcript_support_level": 1,
"aa_start": 410,
"aa_end": null,
"aa_length": 625,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 1409,
"cdna_end": null,
"cdna_length": 6219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.814A>G",
"hgvs_p": "p.Thr272Ala",
"transcript": "ENST00000542407.5",
"protein_id": "ENSP00000442187.2",
"transcript_support_level": 1,
"aa_start": 272,
"aa_end": null,
"aa_length": 487,
"cds_start": 814,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 896,
"cdna_end": null,
"cdna_length": 2979,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "n.1034A>G",
"hgvs_p": null,
"transcript": "ENST00000380176.7",
"protein_id": null,
"transcript_support_level": 1,
"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": 3098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.1228A>G",
"hgvs_p": "p.Thr410Ala",
"transcript": "NM_001256426.2",
"protein_id": "NP_001243355.2",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 625,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 1324,
"cdna_end": null,
"cdna_length": 6130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.1228A>G",
"hgvs_p": "p.Thr410Ala",
"transcript": "ENST00000514743.5",
"protein_id": "ENSP00000424360.1",
"transcript_support_level": 2,
"aa_start": 410,
"aa_end": null,
"aa_length": 625,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 3356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.814A>G",
"hgvs_p": "p.Thr272Ala",
"transcript": "NM_001011513.4",
"protein_id": "NP_001011513.4",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 487,
"cds_start": 814,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 910,
"cdna_end": null,
"cdna_length": 5716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.832A>G",
"hgvs_p": "p.Thr278Ala",
"transcript": "NM_001256427.2",
"protein_id": "NP_001243356.2",
"transcript_support_level": null,
"aa_start": 278,
"aa_end": null,
"aa_length": 483,
"cds_start": 832,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 928,
"cdna_end": null,
"cdna_length": 3745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.832A>G",
"hgvs_p": "p.Thr278Ala",
"transcript": "ENST00000503974.5",
"protein_id": "ENSP00000424297.1",
"transcript_support_level": 2,
"aa_start": 278,
"aa_end": null,
"aa_length": 483,
"cds_start": 832,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 935,
"cdna_end": null,
"cdna_length": 2081,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.775A>G",
"hgvs_p": "p.Thr259Ala",
"transcript": "NM_001256428.2",
"protein_id": "NP_001243357.2",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 474,
"cds_start": 775,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 1085,
"cdna_end": null,
"cdna_length": 5891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.166A>G",
"hgvs_p": "p.Thr56Ala",
"transcript": "NM_001256425.2",
"protein_id": "NP_001243354.2",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 271,
"cds_start": 166,
"cds_end": null,
"cds_length": 816,
"cdna_start": 818,
"cdna_end": null,
"cdna_length": 5624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "c.166A>G",
"hgvs_p": "p.Thr56Ala",
"transcript": "ENST00000437932.5",
"protein_id": "ENSP00000398469.2",
"transcript_support_level": 5,
"aa_start": 56,
"aa_end": null,
"aa_length": 271,
"cds_start": 166,
"cds_end": null,
"cds_length": 816,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 5713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "n.367A>G",
"hgvs_p": null,
"transcript": "ENST00000506632.2",
"protein_id": "ENSP00000422528.1",
"transcript_support_level": 3,
"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": 907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "n.*869A>G",
"hgvs_p": null,
"transcript": "ENST00000627587.2",
"protein_id": "ENSP00000486938.1",
"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": 1853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"hgvs_c": "n.*869A>G",
"hgvs_p": null,
"transcript": "ENST00000627587.2",
"protein_id": "ENSP00000486938.1",
"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": 1853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDLIM5",
"gene_hgnc_id": 17468,
"dbsnp": "rs7690296",
"frequency_reference_population": 0.42126387,
"hom_count_reference_population": 147689,
"allele_count_reference_population": 676923,
"gnomad_exomes_af": 0.426918,
"gnomad_genomes_af": 0.367152,
"gnomad_exomes_ac": 621113,
"gnomad_genomes_ac": 55810,
"gnomad_exomes_homalt": 136396,
"gnomad_genomes_homalt": 11293,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00001284100471821148,
"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": 0.0547,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.442,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000317968.9",
"gene_symbol": "PDLIM5",
"hgnc_id": 17468,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1141A>G",
"hgvs_p": "p.Thr381Ala"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}