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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: 8-74320979-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=74320979&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 74320979,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_020647.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH1",
"gene_hgnc_id": 14201,
"hgvs_c": "c.309C>T",
"hgvs_p": "p.Pro103Pro",
"transcript": "NM_020647.4",
"protein_id": "NP_065698.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 661,
"cds_start": 309,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 4590,
"mane_select": "ENST00000342232.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH1",
"gene_hgnc_id": 14201,
"hgvs_c": "c.309C>T",
"hgvs_p": "p.Pro103Pro",
"transcript": "ENST00000342232.5",
"protein_id": "ENSP00000344488.4",
"transcript_support_level": 1,
"aa_start": 103,
"aa_end": null,
"aa_length": 661,
"cds_start": 309,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 4590,
"mane_select": "NM_020647.4",
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "JPH1",
"gene_hgnc_id": 14201,
"hgvs_c": "n.14+295C>T",
"hgvs_p": null,
"transcript": "ENST00000519947.1",
"protein_id": "ENSP00000429652.1",
"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": 1651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH1",
"gene_hgnc_id": 14201,
"hgvs_c": "c.309C>T",
"hgvs_p": "p.Pro103Pro",
"transcript": "NM_001317830.2",
"protein_id": "NP_001304759.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 661,
"cds_start": 309,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 4310,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH1",
"gene_hgnc_id": 14201,
"hgvs_c": "c.309C>T",
"hgvs_p": "p.Pro103Pro",
"transcript": "NM_001363050.1",
"protein_id": "NP_001349979.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 661,
"cds_start": 309,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 3985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH1",
"gene_hgnc_id": 14201,
"hgvs_c": "c.309C>T",
"hgvs_p": "p.Pro103Pro",
"transcript": "NM_001363051.1",
"protein_id": "NP_001349980.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 661,
"cds_start": 309,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 4134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JPH1",
"gene_hgnc_id": 14201,
"hgvs_c": "c.309C>T",
"hgvs_p": "p.Pro103Pro",
"transcript": "XM_047421996.1",
"protein_id": "XP_047277952.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 661,
"cds_start": 309,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 4762,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GDAP1",
"gene_hgnc_id": 15968,
"hgvs_c": "c.-18+18G>A",
"hgvs_p": null,
"transcript": "ENST00000675821.1",
"protein_id": "ENSP00000502198.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": -4,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3606,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GDAP1",
"gene_hgnc_id": 15968,
"hgvs_c": "c.-18+61G>A",
"hgvs_p": null,
"transcript": "ENST00000676377.1",
"protein_id": "ENSP00000502756.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": -4,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3338,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GDAP1",
"gene_hgnc_id": 15968,
"hgvs_c": "n.340+18G>A",
"hgvs_p": null,
"transcript": "ENST00000521096.6",
"protein_id": null,
"transcript_support_level": 3,
"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": 3390,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GDAP1",
"gene_hgnc_id": 15968,
"hgvs_c": "c.-284G>A",
"hgvs_p": null,
"transcript": "ENST00000675220.1",
"protein_id": "ENSP00000502588.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": -4,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "JPH1",
"gene_hgnc_id": 14201,
"dbsnp": "rs79761162",
"frequency_reference_population": 0.0041721603,
"hom_count_reference_population": 261,
"allele_count_reference_population": 6721,
"gnomad_exomes_af": 0.00228898,
"gnomad_genomes_af": 0.0222225,
"gnomad_exomes_ac": 3339,
"gnomad_genomes_ac": 3382,
"gnomad_exomes_homalt": 138,
"gnomad_genomes_homalt": 123,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"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": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.705,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_020647.4",
"gene_symbol": "JPH1",
"hgnc_id": 14201,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.309C>T",
"hgvs_p": "p.Pro103Pro"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000521096.6",
"gene_symbol": "GDAP1",
"hgnc_id": 15968,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "n.340+18G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}