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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: 6-160706469-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=160706469&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 160706469,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000301.5",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "c.112A>G",
"hgvs_p": "p.Lys38Glu",
"transcript": "NM_000301.5",
"protein_id": "NP_000292.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 810,
"cds_start": 112,
"cds_end": null,
"cds_length": 2433,
"cdna_start": 173,
"cdna_end": null,
"cdna_length": 3530,
"mane_select": "ENST00000308192.14",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "c.112A>G",
"hgvs_p": "p.Lys38Glu",
"transcript": "ENST00000308192.14",
"protein_id": "ENSP00000308938.9",
"transcript_support_level": 1,
"aa_start": 38,
"aa_end": null,
"aa_length": 810,
"cds_start": 112,
"cds_end": null,
"cds_length": 2433,
"cdna_start": 173,
"cdna_end": null,
"cdna_length": 3530,
"mane_select": "NM_000301.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "c.112A>G",
"hgvs_p": "p.Lys38Glu",
"transcript": "ENST00000366924.6",
"protein_id": "ENSP00000355891.2",
"transcript_support_level": 1,
"aa_start": 38,
"aa_end": null,
"aa_length": 136,
"cds_start": 112,
"cds_end": null,
"cds_length": 411,
"cdna_start": 179,
"cdna_end": null,
"cdna_length": 1166,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "n.1082A>G",
"hgvs_p": null,
"transcript": "ENST00000484367.5",
"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": 2465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "c.-114A>G",
"hgvs_p": null,
"transcript": "ENST00000494325.2",
"protein_id": "ENSP00000516620.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": -4,
"cds_end": null,
"cds_length": 186,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1083,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "c.112A>G",
"hgvs_p": "p.Lys38Glu",
"transcript": "ENST00000418964.2",
"protein_id": "ENSP00000389424.2",
"transcript_support_level": 4,
"aa_start": 38,
"aa_end": null,
"aa_length": 827,
"cds_start": 112,
"cds_end": null,
"cds_length": 2484,
"cdna_start": 223,
"cdna_end": null,
"cdna_length": 3580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "c.112A>G",
"hgvs_p": "p.Lys38Glu",
"transcript": "NM_001168338.1",
"protein_id": "NP_001161810.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 136,
"cds_start": 112,
"cds_end": null,
"cds_length": 411,
"cdna_start": 224,
"cdna_end": null,
"cdna_length": 1200,
"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": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "n.149A>G",
"hgvs_p": null,
"transcript": "ENST00000462918.5",
"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": 835,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "n.95A>G",
"hgvs_p": null,
"transcript": "ENST00000471691.1",
"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": 786,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "n.125A>G",
"hgvs_p": null,
"transcript": "ENST00000483038.5",
"protein_id": null,
"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": 757,
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "n.112A>G",
"hgvs_p": null,
"transcript": "ENST00000706906.1",
"protein_id": "ENSP00000516618.1",
"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": 5213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "c.-114A>G",
"hgvs_p": null,
"transcript": "ENST00000494325.2",
"protein_id": "ENSP00000516620.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": -4,
"cds_end": null,
"cds_length": 186,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1083,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"hgvs_c": "c.49+4116A>G",
"hgvs_p": null,
"transcript": "ENST00000297289.9",
"protein_id": "ENSP00000516619.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 461,
"cds_start": -4,
"cds_end": null,
"cds_length": 1386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLG",
"gene_hgnc_id": 9071,
"dbsnp": "rs73015965",
"frequency_reference_population": 0.0049769804,
"hom_count_reference_population": 36,
"allele_count_reference_population": 8032,
"gnomad_exomes_af": 0.00520695,
"gnomad_genomes_af": 0.00277045,
"gnomad_exomes_ac": 7610,
"gnomad_genomes_ac": 422,
"gnomad_exomes_homalt": 34,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.19466236233711243,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.642,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1455,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.662,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP5_Very_Strong,BP4,BS1_Supporting",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 2,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong",
"BP4",
"BS1_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000301.5",
"gene_symbol": "PLG",
"hgnc_id": 9071,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.112A>G",
"hgvs_p": "p.Lys38Glu"
}
],
"clinvar_disease": " 4, hereditary, susceptibility to, type I,Angioedema,Deep venous thrombosis,Otitis media,Plasminogen deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:9 LP:4 US:2 B:1",
"phenotype_combined": "Plasminogen deficiency, type I|not provided|Otitis media, susceptibility to|Deep venous thrombosis|Angioedema, hereditary, 4;Plasminogen deficiency, type I",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}