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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: 20-62139146-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=62139146&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 62139146,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002792.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.400G>A",
"hgvs_p": "p.Val134Met",
"transcript": "NM_002792.4",
"protein_id": "NP_002783.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 248,
"cds_start": 400,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000370873.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002792.4"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.400G>A",
"hgvs_p": "p.Val134Met",
"transcript": "ENST00000370873.9",
"protein_id": "ENSP00000359910.4",
"transcript_support_level": 1,
"aa_start": 134,
"aa_end": null,
"aa_length": 248,
"cds_start": 400,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002792.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370873.9"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.388G>A",
"hgvs_p": "p.Val130Met",
"transcript": "ENST00000867843.1",
"protein_id": "ENSP00000537902.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 244,
"cds_start": 388,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867843.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.382G>A",
"hgvs_p": "p.Val128Met",
"transcript": "ENST00000931805.1",
"protein_id": "ENSP00000601864.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 242,
"cds_start": 382,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931805.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.400G>A",
"hgvs_p": "p.Val134Met",
"transcript": "ENST00000867844.1",
"protein_id": "ENSP00000537903.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 227,
"cds_start": 400,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867844.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.400G>A",
"hgvs_p": "p.Val134Met",
"transcript": "ENST00000931802.1",
"protein_id": "ENSP00000601861.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 208,
"cds_start": 400,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931802.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.400G>A",
"hgvs_p": "p.Val134Met",
"transcript": "ENST00000931804.1",
"protein_id": "ENSP00000601863.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 187,
"cds_start": 400,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931804.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.175G>A",
"hgvs_p": "p.Val59Met",
"transcript": "ENST00000442551.5",
"protein_id": "ENSP00000397047.1",
"transcript_support_level": 3,
"aa_start": 59,
"aa_end": null,
"aa_length": 186,
"cds_start": 175,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442551.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.190G>A",
"hgvs_p": "p.Val64Met",
"transcript": "ENST00000370861.1",
"protein_id": "ENSP00000359898.1",
"transcript_support_level": 5,
"aa_start": 64,
"aa_end": null,
"aa_length": 178,
"cds_start": 190,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370861.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.348+635G>A",
"hgvs_p": null,
"transcript": "ENST00000931806.1",
"protein_id": "ENSP00000601865.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 207,
"cds_start": null,
"cds_end": null,
"cds_length": 624,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931806.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.348+635G>A",
"hgvs_p": null,
"transcript": "ENST00000931803.1",
"protein_id": "ENSP00000601862.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 167,
"cds_start": null,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931803.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.97-2197G>A",
"hgvs_p": null,
"transcript": "ENST00000931807.1",
"protein_id": "ENSP00000601866.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 62,
"cds_start": null,
"cds_end": null,
"cds_length": 189,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931807.1"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "n.622G>A",
"hgvs_p": null,
"transcript": "ENST00000484488.5",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000484488.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "n.251G>A",
"hgvs_p": null,
"transcript": "ENST00000486193.1",
"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": "pseudogene",
"feature": "ENST00000486193.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"hgvs_c": "c.*533G>A",
"hgvs_p": null,
"transcript": "ENST00000370858.3",
"protein_id": "ENSP00000359895.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 149,
"cds_start": null,
"cds_end": null,
"cds_length": 450,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370858.3"
}
],
"gene_symbol": "PSMA7",
"gene_hgnc_id": 9536,
"dbsnp": "rs776926070",
"frequency_reference_population": 0.000014869299,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.0000150496,
"gnomad_genomes_af": 0.000013138,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7723129391670227,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.373,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5698,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.37,
"phylop100way_prediction": "Uncertain_significance",
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002792.4",
"gene_symbol": "PSMA7",
"hgnc_id": 9536,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.400G>A",
"hgvs_p": "p.Val134Met"
}
],
"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
}