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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: 5-33963973-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=33963973&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 33963973,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000296589.9",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.606G>C",
"hgvs_p": "p.Trp202Cys",
"transcript": "NM_016180.5",
"protein_id": "NP_057264.4",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 530,
"cds_start": 606,
"cds_end": null,
"cds_length": 1593,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 1728,
"mane_select": "ENST00000296589.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.606G>C",
"hgvs_p": "p.Trp202Cys",
"transcript": "ENST00000296589.9",
"protein_id": "ENSP00000296589.4",
"transcript_support_level": 1,
"aa_start": 202,
"aa_end": null,
"aa_length": 530,
"cds_start": 606,
"cds_end": null,
"cds_length": 1593,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 1728,
"mane_select": "NM_016180.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.606G>C",
"hgvs_p": "p.Trp202Cys",
"transcript": "ENST00000382102.7",
"protein_id": "ENSP00000371534.3",
"transcript_support_level": 1,
"aa_start": 202,
"aa_end": null,
"aa_length": 460,
"cds_start": 606,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 664,
"cdna_end": null,
"cdna_length": 2723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.563-9469G>C",
"hgvs_p": null,
"transcript": "ENST00000509381.1",
"protein_id": "ENSP00000421100.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 243,
"cds_start": -4,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.606G>C",
"hgvs_p": "p.Trp202Cys",
"transcript": "NM_001012509.4",
"protein_id": "NP_001012527.2",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 460,
"cds_start": 606,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 2775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.81G>C",
"hgvs_p": "p.Trp27Cys",
"transcript": "ENST00000510600.1",
"protein_id": "ENSP00000424010.1",
"transcript_support_level": 3,
"aa_start": 27,
"aa_end": null,
"aa_length": 245,
"cds_start": 81,
"cds_end": null,
"cds_length": 738,
"cdna_start": 83,
"cdna_end": null,
"cdna_length": 740,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.606G>C",
"hgvs_p": "p.Trp202Cys",
"transcript": "XM_047417259.1",
"protein_id": "XP_047273215.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 450,
"cds_start": 606,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 1488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.606G>C",
"hgvs_p": "p.Trp202Cys",
"transcript": "XM_047417260.1",
"protein_id": "XP_047273216.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 365,
"cds_start": 606,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 2301,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "n.408G>C",
"hgvs_p": null,
"transcript": "ENST00000505056.1",
"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": 739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"hgvs_c": "c.563-9469G>C",
"hgvs_p": null,
"transcript": "NM_001297417.4",
"protein_id": "NP_001284346.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 243,
"cds_start": -4,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC45A2",
"gene_hgnc_id": 16472,
"dbsnp": "rs146802593",
"frequency_reference_population": 0.0001846452,
"hom_count_reference_population": 0,
"allele_count_reference_population": 298,
"gnomad_exomes_af": 0.000187444,
"gnomad_genomes_af": 0.000157752,
"gnomad_exomes_ac": 274,
"gnomad_genomes_ac": 24,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8507063388824463,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.816,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9705,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.49,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.13,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.08,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000296589.9",
"gene_symbol": "SLC45A2",
"hgnc_id": 16472,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.606G>C",
"hgvs_p": "p.Trp202Cys"
}
],
"clinvar_disease": "Albinism or congenital nystagmus,Inborn genetic diseases,Oculocutaneous albinism type 4,SLC45A2-related disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:6",
"phenotype_combined": "Inborn genetic diseases|not provided|Oculocutaneous albinism type 4|SLC45A2-related disorder|Albinism or congenital nystagmus",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}