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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: 2-196926586-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=196926586&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 196926586,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000354764.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.31C>T",
"hgvs_p": "p.Leu11Leu",
"transcript": "NM_024989.4",
"protein_id": "NP_079265.2",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 922,
"cds_start": 31,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 11090,
"mane_select": "ENST00000354764.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.31C>T",
"hgvs_p": "p.Leu11Leu",
"transcript": "ENST00000354764.9",
"protein_id": "ENSP00000346809.3",
"transcript_support_level": 1,
"aa_start": 11,
"aa_end": null,
"aa_length": 922,
"cds_start": 31,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 11090,
"mane_select": "NM_024989.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.31C>T",
"hgvs_p": null,
"transcript": "ENST00000423035.5",
"protein_id": "ENSP00000415405.1",
"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": 8942,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.207+1004C>T",
"hgvs_p": null,
"transcript": "ENST00000485830.1",
"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": 1222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.-576C>T",
"hgvs_p": null,
"transcript": "NM_001321099.2",
"protein_id": "NP_001308028.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 748,
"cds_start": -4,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.-1081C>T",
"hgvs_p": null,
"transcript": "NM_001321100.2",
"protein_id": "NP_001308029.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 533,
"cds_start": -4,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.31C>T",
"hgvs_p": "p.Leu11Leu",
"transcript": "ENST00000409475.5",
"protein_id": "ENSP00000387028.1",
"transcript_support_level": 2,
"aa_start": 11,
"aa_end": null,
"aa_length": 592,
"cds_start": 31,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 145,
"cdna_end": null,
"cdna_length": 2443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.31C>T",
"hgvs_p": "p.Leu11Leu",
"transcript": "ENST00000374738.3",
"protein_id": "ENSP00000363870.3",
"transcript_support_level": 5,
"aa_start": 11,
"aa_end": null,
"aa_length": 181,
"cds_start": 31,
"cds_end": null,
"cds_length": 548,
"cdna_start": 160,
"cdna_end": null,
"cdna_length": 677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.31C>T",
"hgvs_p": "p.Leu11Leu",
"transcript": "XM_047445910.1",
"protein_id": "XP_047301866.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 452,
"cds_start": 31,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 122,
"cdna_end": null,
"cdna_length": 3279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.155C>T",
"hgvs_p": null,
"transcript": "ENST00000470179.5",
"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": 2874,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.122C>T",
"hgvs_p": null,
"transcript": "XR_001738960.2",
"protein_id": null,
"transcript_support_level": null,
"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": 1528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.122C>T",
"hgvs_p": null,
"transcript": "XR_007082522.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2049,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.-576C>T",
"hgvs_p": null,
"transcript": "NM_001321099.2",
"protein_id": "NP_001308028.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 748,
"cds_start": -4,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.-1081C>T",
"hgvs_p": null,
"transcript": "NM_001321100.2",
"protein_id": "NP_001308029.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 533,
"cds_start": -4,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.21+1004C>T",
"hgvs_p": null,
"transcript": "ENST00000409188.5",
"protein_id": "ENSP00000386802.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 304,
"cds_start": -4,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"dbsnp": "rs375123215",
"frequency_reference_population": 0.000021683749,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000218895,
"gnomad_genomes_af": 0.0000197081,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6299999952316284,
"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": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.455,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000354764.9",
"gene_symbol": "PGAP1",
"hgnc_id": 25712,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.31C>T",
"hgvs_p": "p.Leu11Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}