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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: 16-16161567-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=16161567&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 16161567,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000205557.12",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "c.3507-3C>T",
"hgvs_p": null,
"transcript": "NM_001171.6",
"protein_id": "NP_001162.5",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1503,
"cds_start": -4,
"cds_end": null,
"cds_length": 4512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5140,
"mane_select": "ENST00000205557.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "c.3507-3C>T",
"hgvs_p": null,
"transcript": "ENST00000205557.12",
"protein_id": "ENSP00000205557.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1503,
"cds_start": -4,
"cds_end": null,
"cds_length": 4512,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5140,
"mane_select": "NM_001171.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "c.3474-3C>T",
"hgvs_p": null,
"transcript": "NM_001440309.1",
"protein_id": "NP_001427238.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1492,
"cds_start": -4,
"cds_end": null,
"cds_length": 4479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5107,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "c.3339-3C>T",
"hgvs_p": null,
"transcript": "NM_001440310.1",
"protein_id": "NP_001427239.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1447,
"cds_start": -4,
"cds_end": null,
"cds_length": 4344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "c.3165-3C>T",
"hgvs_p": null,
"transcript": "NM_001351800.1",
"protein_id": "NP_001338729.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1389,
"cds_start": -4,
"cds_end": null,
"cds_length": 4170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "n.*516-3C>T",
"hgvs_p": null,
"transcript": "ENST00000456970.6",
"protein_id": "ENSP00000405002.2",
"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": 4137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "n.3507-3C>T",
"hgvs_p": null,
"transcript": "ENST00000622290.5",
"protein_id": "ENSP00000483331.2",
"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": 5203,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "n.3169-3C>T",
"hgvs_p": null,
"transcript": "NR_147784.1",
"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": 4742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "n.3425-3C>T",
"hgvs_p": null,
"transcript": "NR_199641.1",
"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": 5227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "n.3567-3C>T",
"hgvs_p": null,
"transcript": "NR_199642.1",
"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": 5203,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"hgvs_c": "n.3367-3C>T",
"hgvs_p": null,
"transcript": "NR_199643.1",
"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": 5003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCC6",
"gene_hgnc_id": 57,
"dbsnp": "rs41278172",
"frequency_reference_population": 0.017881883,
"hom_count_reference_population": 357,
"allele_count_reference_population": 28859,
"gnomad_exomes_af": 0.0181428,
"gnomad_genomes_af": 0.0153779,
"gnomad_exomes_ac": 26517,
"gnomad_genomes_ac": 2342,
"gnomad_exomes_homalt": 326,
"gnomad_genomes_homalt": 31,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.41999998688697815,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.6520000100135803,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.364,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0228291505749774,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000205557.12",
"gene_symbol": "ABCC6",
"hgnc_id": 57,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3507-3C>T",
"hgvs_p": null
}
],
"clinvar_disease": " 2, forme fruste, generalized, of infancy,Arterial calcification,Autosomal recessive inherited pseudoxanthoma elasticum,Finnish congenital nephrotic syndrome,Pseudoxanthoma elasticum,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:8",
"phenotype_combined": "not specified|Autosomal recessive inherited pseudoxanthoma elasticum|Finnish congenital nephrotic syndrome|not provided|Arterial calcification, generalized, of infancy, 2|Autosomal recessive inherited pseudoxanthoma elasticum;Pseudoxanthoma elasticum, forme fruste;Arterial calcification, generalized, of infancy, 2|Pseudoxanthoma elasticum, forme fruste",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}