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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: 17-39986627-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=39986627&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 39986627,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002809.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "NM_002809.4",
"protein_id": "NP_002800.2",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 534,
"cds_start": 464,
"cds_end": null,
"cds_length": 1605,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264639.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002809.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000264639.9",
"protein_id": "ENSP00000264639.4",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 534,
"cds_start": 464,
"cds_end": null,
"cds_length": 1605,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002809.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264639.9"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000916285.1",
"protein_id": "ENSP00000586344.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 532,
"cds_start": 464,
"cds_end": null,
"cds_length": 1599,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916285.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.437C>T",
"hgvs_p": "p.Ala146Val",
"transcript": "ENST00000916290.1",
"protein_id": "ENSP00000586349.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 525,
"cds_start": 437,
"cds_end": null,
"cds_length": 1578,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916290.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000871890.1",
"protein_id": "ENSP00000541949.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 519,
"cds_start": 464,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871890.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000916286.1",
"protein_id": "ENSP00000586345.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 517,
"cds_start": 464,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916286.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000916288.1",
"protein_id": "ENSP00000586347.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 494,
"cds_start": 464,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916288.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000871889.1",
"protein_id": "ENSP00000541948.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 482,
"cds_start": 464,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871889.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000916287.1",
"protein_id": "ENSP00000586346.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 442,
"cds_start": 464,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916287.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000871888.1",
"protein_id": "ENSP00000541947.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 421,
"cds_start": 464,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871888.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val",
"transcript": "ENST00000916289.1",
"protein_id": "ENSP00000586348.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 369,
"cds_start": 464,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916289.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.17C>T",
"hgvs_p": "p.Ala6Val",
"transcript": "ENST00000540504.2",
"protein_id": "ENSP00000444980.2",
"transcript_support_level": 3,
"aa_start": 6,
"aa_end": null,
"aa_length": 116,
"cds_start": 17,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540504.2"
},
{
"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": 11,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "c.412-2056C>T",
"hgvs_p": null,
"transcript": "ENST00000871891.1",
"protein_id": "ENSP00000541950.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 488,
"cds_start": null,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871891.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "n.199C>T",
"hgvs_p": null,
"transcript": "ENST00000415039.7",
"protein_id": "ENSP00000407410.3",
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000415039.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD3-AS1",
"gene_hgnc_id": 58140,
"hgvs_c": "n.995G>A",
"hgvs_p": null,
"transcript": "ENST00000801108.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000801108.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"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": "PSMD3",
"gene_hgnc_id": 9560,
"hgvs_c": "n.-57C>T",
"hgvs_p": null,
"transcript": "ENST00000580980.1",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000580980.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124904000",
"gene_hgnc_id": null,
"hgvs_c": "n.*71G>A",
"hgvs_p": null,
"transcript": "XR_007065751.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007065751.1"
}
],
"gene_symbol": "PSMD3",
"gene_hgnc_id": 9560,
"dbsnp": "rs777827638",
"frequency_reference_population": 0.000029120523,
"hom_count_reference_population": 0,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000300985,
"gnomad_genomes_af": 0.0000197218,
"gnomad_exomes_ac": 44,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7016209959983826,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.54,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1942,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.648,
"phylop100way_prediction": "Pathogenic",
"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": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002809.4",
"gene_symbol": "PSMD3",
"hgnc_id": 9560,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Ala155Val"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000801108.1",
"gene_symbol": "PSMD3-AS1",
"hgnc_id": 58140,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.995G>A",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007065751.1",
"gene_symbol": "LOC124904000",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*71G>A",
"hgvs_p": null
}
],
"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
}