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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: 1-10413139-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=10413139&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 10413139,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_002631.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Asp244Asp",
"transcript": "NM_002631.4",
"protein_id": "NP_002622.2",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 483,
"cds_start": 732,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000270776.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002631.4"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Asp244Asp",
"transcript": "ENST00000270776.13",
"protein_id": "ENSP00000270776.8",
"transcript_support_level": 1,
"aa_start": 244,
"aa_end": null,
"aa_length": 483,
"cds_start": 732,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002631.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000270776.13"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Asp244Asp",
"transcript": "ENST00000863229.1",
"protein_id": "ENSP00000533288.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 482,
"cds_start": 732,
"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": "ENST00000863229.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.729C>T",
"hgvs_p": "p.Asp243Asp",
"transcript": "ENST00000863230.1",
"protein_id": "ENSP00000533289.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 482,
"cds_start": 729,
"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": "ENST00000863230.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.729C>T",
"hgvs_p": "p.Asp243Asp",
"transcript": "ENST00000922425.1",
"protein_id": "ENSP00000592484.1",
"transcript_support_level": null,
"aa_start": 243,
"aa_end": null,
"aa_length": 482,
"cds_start": 729,
"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": "ENST00000922425.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Asp244Asp",
"transcript": "ENST00000957131.1",
"protein_id": "ENSP00000627190.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 481,
"cds_start": 732,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957131.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.693C>T",
"hgvs_p": "p.Asp231Asp",
"transcript": "NM_001304452.2",
"protein_id": "NP_001291381.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 470,
"cds_start": 693,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304452.2"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.666C>T",
"hgvs_p": "p.Asp222Asp",
"transcript": "NM_001304451.2",
"protein_id": "NP_001291380.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 461,
"cds_start": 666,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304451.2"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Asp244Asp",
"transcript": "ENST00000922426.1",
"protein_id": "ENSP00000592485.1",
"transcript_support_level": null,
"aa_start": 244,
"aa_end": null,
"aa_length": 442,
"cds_start": 732,
"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": "ENST00000922426.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.552C>T",
"hgvs_p": "p.Asp184Asp",
"transcript": "ENST00000863228.1",
"protein_id": "ENSP00000533287.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 423,
"cds_start": 552,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863228.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.489C>T",
"hgvs_p": "p.Asp163Asp",
"transcript": "ENST00000957132.1",
"protein_id": "ENSP00000627191.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 402,
"cds_start": 489,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957132.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.486C>T",
"hgvs_p": "p.Asp162Asp",
"transcript": "ENST00000957133.1",
"protein_id": "ENSP00000627192.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 401,
"cds_start": 486,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957133.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.477C>T",
"hgvs_p": "p.Asp159Asp",
"transcript": "ENST00000922427.1",
"protein_id": "ENSP00000592486.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 398,
"cds_start": 477,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922427.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.486C>T",
"hgvs_p": "p.Asp162Asp",
"transcript": "ENST00000922428.1",
"protein_id": "ENSP00000592487.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 360,
"cds_start": 486,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922428.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.654C>T",
"hgvs_p": "p.Asp218Asp",
"transcript": "ENST00000460189.1",
"protein_id": "ENSP00000467362.1",
"transcript_support_level": 2,
"aa_start": 218,
"aa_end": null,
"aa_length": 254,
"cds_start": 654,
"cds_end": null,
"cds_length": 766,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000460189.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "c.297C>T",
"hgvs_p": "p.Asp99Asp",
"transcript": "ENST00000483936.5",
"protein_id": "ENSP00000466156.1",
"transcript_support_level": 5,
"aa_start": 99,
"aa_end": null,
"aa_length": 223,
"cds_start": 297,
"cds_end": null,
"cds_length": 674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000483936.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"hgvs_c": "n.306C>T",
"hgvs_p": null,
"transcript": "ENST00000493288.1",
"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": "retained_intron",
"feature": "ENST00000493288.1"
}
],
"gene_symbol": "PGD",
"gene_hgnc_id": 8891,
"dbsnp": "rs2229687",
"frequency_reference_population": 0.3251365,
"hom_count_reference_population": 85981,
"allele_count_reference_population": 524520,
"gnomad_exomes_af": 0.324614,
"gnomad_genomes_af": 0.330157,
"gnomad_exomes_ac": 474317,
"gnomad_genomes_ac": 50203,
"gnomad_exomes_homalt": 77556,
"gnomad_genomes_homalt": 8425,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8199999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.82,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.613,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_002631.4",
"gene_symbol": "PGD",
"hgnc_id": 8891,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.732C>T",
"hgvs_p": "p.Asp244Asp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}