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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: 3-184302754-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=184302754&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 184302754,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000310118.9",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "c.939G>T",
"hgvs_p": "p.Glu313Asp",
"transcript": "NM_002808.5",
"protein_id": "NP_002799.3",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 908,
"cds_start": 939,
"cds_end": null,
"cds_length": 2727,
"cdna_start": 965,
"cdna_end": null,
"cdna_length": 2913,
"mane_select": "ENST00000310118.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "c.939G>T",
"hgvs_p": "p.Glu313Asp",
"transcript": "ENST00000310118.9",
"protein_id": "ENSP00000310129.4",
"transcript_support_level": 1,
"aa_start": 313,
"aa_end": null,
"aa_length": 908,
"cds_start": 939,
"cds_end": null,
"cds_length": 2727,
"cdna_start": 965,
"cdna_end": null,
"cdna_length": 2913,
"mane_select": "NM_002808.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "c.549G>T",
"hgvs_p": "p.Glu183Asp",
"transcript": "NM_001278708.2",
"protein_id": "NP_001265637.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 778,
"cds_start": 549,
"cds_end": null,
"cds_length": 2337,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 2635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "c.549G>T",
"hgvs_p": "p.Glu183Asp",
"transcript": "ENST00000439383.5",
"protein_id": "ENSP00000416028.1",
"transcript_support_level": 2,
"aa_start": 183,
"aa_end": null,
"aa_length": 778,
"cds_start": 549,
"cds_end": null,
"cds_length": 2337,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 2633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "c.462G>T",
"hgvs_p": "p.Glu154Asp",
"transcript": "NM_001278709.2",
"protein_id": "NP_001265638.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 749,
"cds_start": 462,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 2624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "c.462G>T",
"hgvs_p": "p.Glu154Asp",
"transcript": "ENST00000435761.5",
"protein_id": "ENSP00000402618.1",
"transcript_support_level": 2,
"aa_start": 154,
"aa_end": null,
"aa_length": 749,
"cds_start": 462,
"cds_end": null,
"cds_length": 2250,
"cdna_start": 676,
"cdna_end": null,
"cdna_length": 2574,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "n.*374G>T",
"hgvs_p": null,
"transcript": "ENST00000445558.6",
"protein_id": "ENSP00000407259.2",
"transcript_support_level": 5,
"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": 825,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "n.15G>T",
"hgvs_p": null,
"transcript": "ENST00000460628.1",
"protein_id": null,
"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": 565,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "n.585G>T",
"hgvs_p": null,
"transcript": "ENST00000485937.1",
"protein_id": null,
"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": 603,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "n.575G>T",
"hgvs_p": null,
"transcript": "ENST00000491149.5",
"protein_id": null,
"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": 895,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "n.*374G>T",
"hgvs_p": null,
"transcript": "ENST00000445558.6",
"protein_id": "ENSP00000407259.2",
"transcript_support_level": 5,
"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": 825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"hgvs_c": "c.*62G>T",
"hgvs_p": null,
"transcript": "ENST00000417952.5",
"protein_id": "ENSP00000414061.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 216,
"cds_start": -4,
"cds_end": null,
"cds_length": 652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PSMD2",
"gene_hgnc_id": 9559,
"dbsnp": "rs11545169",
"frequency_reference_population": 0.14662158,
"hom_count_reference_population": 18520,
"allele_count_reference_population": 236649,
"gnomad_exomes_af": 0.150085,
"gnomad_genomes_af": 0.113337,
"gnomad_exomes_ac": 219407,
"gnomad_genomes_ac": 17242,
"gnomad_exomes_homalt": 17261,
"gnomad_genomes_homalt": 1259,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0014640390872955322,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.2,
"revel_prediction": "Benign",
"alphamissense_score": 0.0707,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.44,
"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": "ENST00000310118.9",
"gene_symbol": "PSMD2",
"hgnc_id": 9559,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.939G>T",
"hgvs_p": "p.Glu313Asp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}