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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: 16-1792208-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=1792208&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 1792208,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_001146006.2",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.210T>C",
"hgvs_p": "p.Asp70Asp",
"transcript": "NM_004970.3",
"protein_id": "NP_004961.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 605,
"cds_start": 210,
"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": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.210T>C",
"hgvs_p": "p.Asp70Asp",
"transcript": "ENST00000215539.4",
"protein_id": "ENSP00000215539.3",
"transcript_support_level": 1,
"aa_start": 70,
"aa_end": null,
"aa_length": 605,
"cds_start": 210,
"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": "M",
"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.242T>C",
"hgvs_p": "p.Met81Thr",
"transcript": "ENST00000568221.1",
"protein_id": "ENSP00000456923.1",
"transcript_support_level": 4,
"aa_start": 81,
"aa_end": null,
"aa_length": 131,
"cds_start": 242,
"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"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.324T>C",
"hgvs_p": "p.Asp108Asp",
"transcript": "NM_001146006.2",
"protein_id": "NP_001139478.1",
"transcript_support_level": null,
"aa_start": 108,
"aa_end": null,
"aa_length": 643,
"cds_start": 324,
"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": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.324T>C",
"hgvs_p": "p.Asp108Asp",
"transcript": "ENST00000415638.3",
"protein_id": "ENSP00000416683.3",
"transcript_support_level": 2,
"aa_start": 108,
"aa_end": null,
"aa_length": 643,
"cds_start": 324,
"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": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.285T>C",
"hgvs_p": "p.Asp95Asp",
"transcript": "ENST00000897144.1",
"protein_id": "ENSP00000567203.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 630,
"cds_start": 285,
"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": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.207T>C",
"hgvs_p": "p.Asp69Asp",
"transcript": "ENST00000897145.1",
"protein_id": "ENSP00000567204.1",
"transcript_support_level": null,
"aa_start": 69,
"aa_end": null,
"aa_length": 604,
"cds_start": 207,
"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+1429T>C",
"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.264T>C",
"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"
}
],
"gene_symbol": "IGFALS",
"gene_hgnc_id": 5468,
"dbsnp": "rs3751893",
"frequency_reference_population": 0.80798864,
"hom_count_reference_population": 526395,
"allele_count_reference_population": 1300002,
"gnomad_exomes_af": 0.808052,
"gnomad_genomes_af": 0.807382,
"gnomad_exomes_ac": 1177070,
"gnomad_genomes_ac": 122932,
"gnomad_exomes_homalt": 476598,
"gnomad_genomes_homalt": 49797,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 9.063880384019285e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.0684,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -1.02,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.888,
"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_001146006.2",
"gene_symbol": "IGFALS",
"hgnc_id": 5468,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.324T>C",
"hgvs_p": "p.Asp108Asp"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000569769.1",
"gene_symbol": "SPSB3",
"hgnc_id": 30629,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-13+1429T>C",
"hgvs_p": null
}
],
"clinvar_disease": "IGFALS-related disorder,Short stature due to primary acid-labile subunit deficiency,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Short stature due to primary acid-labile subunit deficiency|IGFALS-related disorder|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}