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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: 16-1791784-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=1791784&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 1791784,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001146006.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Ala212Thr",
"transcript": "NM_004970.3",
"protein_id": "NP_004961.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 605,
"cds_start": 634,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000215539.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004970.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Ala212Thr",
"transcript": "ENST00000215539.4",
"protein_id": "ENSP00000215539.3",
"transcript_support_level": 1,
"aa_start": 212,
"aa_end": null,
"aa_length": 605,
"cds_start": 634,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004970.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000215539.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"hgvs_c": "c.748G>A",
"hgvs_p": "p.Ala250Thr",
"transcript": "NM_001146006.2",
"protein_id": "NP_001139478.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 643,
"cds_start": 748,
"cds_end": null,
"cds_length": 1932,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001146006.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"hgvs_c": "c.748G>A",
"hgvs_p": "p.Ala250Thr",
"transcript": "ENST00000415638.3",
"protein_id": "ENSP00000416683.3",
"transcript_support_level": 2,
"aa_start": 250,
"aa_end": null,
"aa_length": 643,
"cds_start": 748,
"cds_end": null,
"cds_length": 1932,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415638.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"hgvs_c": "c.709G>A",
"hgvs_p": "p.Ala237Thr",
"transcript": "ENST00000897144.1",
"protein_id": "ENSP00000567203.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 630,
"cds_start": 709,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897144.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"hgvs_c": "c.631G>A",
"hgvs_p": "p.Ala211Thr",
"transcript": "ENST00000897145.1",
"protein_id": "ENSP00000567204.1",
"transcript_support_level": null,
"aa_start": 211,
"aa_end": null,
"aa_length": 604,
"cds_start": 631,
"cds_end": null,
"cds_length": 1815,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897145.1"
},
{
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPSB3",
"gene_hgnc_id": 30629,
"hgvs_c": "c.-13+1853G>A",
"hgvs_p": null,
"transcript": "ENST00000569769.1",
"protein_id": "ENSP00000455098.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 167,
"cds_start": null,
"cds_end": null,
"cds_length": 504,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000569769.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"hgvs_c": "n.688G>A",
"hgvs_p": null,
"transcript": "NR_027389.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_027389.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"hgvs_c": "c.*270G>A",
"hgvs_p": null,
"transcript": "ENST00000568221.1",
"protein_id": "ENSP00000456923.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 131,
"cds_start": null,
"cds_end": null,
"cds_length": 396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000568221.1"
}
],
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"dbsnp": "rs368097770",
"frequency_reference_population": 0.00050632714,
"hom_count_reference_population": 0,
"allele_count_reference_population": 784,
"gnomad_exomes_af": 0.000527191,
"gnomad_genomes_af": 0.00031511,
"gnomad_exomes_ac": 736,
"gnomad_genomes_ac": 48,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03124260902404785,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.17,
"revel_prediction": "Benign",
"alphamissense_score": 0.0869,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.268,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_001146006.2",
"gene_symbol": "IGFALS",
"hgnc_id": 5468,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.748G>A",
"hgvs_p": "p.Ala250Thr"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000569769.1",
"gene_symbol": "SPSB3",
"hgnc_id": 30629,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-13+1853G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Short stature due to primary acid-labile subunit deficiency,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "Short stature due to primary acid-labile subunit deficiency|not specified|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}