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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: 12-56235666-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=56235666&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 56235666,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000454355.7",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "NM_173596.3",
"protein_id": "NP_775867.2",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 1980,
"mane_select": "ENST00000454355.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "ENST00000454355.7",
"protein_id": "ENSP00000405360.2",
"transcript_support_level": 1,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 1980,
"mane_select": "NM_173596.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "ENST00000266980.8",
"protein_id": "ENSP00000266980.4",
"transcript_support_level": 1,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 2031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "NM_001135195.1",
"protein_id": "NP_001128667.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1139,
"cdna_end": null,
"cdna_length": 1966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "XM_005268803.3",
"protein_id": "XP_005268860.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 1881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "XM_011538199.3",
"protein_id": "XP_011536501.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1180,
"cdna_end": null,
"cdna_length": 2007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "XM_011538200.3",
"protein_id": "XP_011536502.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1110,
"cdna_end": null,
"cdna_length": 1937,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "XM_011538201.3",
"protein_id": "XP_011536503.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1097,
"cdna_end": null,
"cdna_length": 1924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "XM_047428713.1",
"protein_id": "XP_047284669.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 2091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "XM_047428714.1",
"protein_id": "XP_047284670.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1291,
"cdna_end": null,
"cdna_length": 2118,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "XM_047428715.1",
"protein_id": "XP_047284671.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 540,
"cds_start": 911,
"cds_end": null,
"cds_length": 1623,
"cdna_start": 1124,
"cdna_end": null,
"cdna_length": 1951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg",
"transcript": "XM_047428716.1",
"protein_id": "XP_047284672.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 474,
"cds_start": 911,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 1900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "n.780T>G",
"hgvs_p": null,
"transcript": "ENST00000481103.5",
"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": 926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"hgvs_c": "n.1264T>G",
"hgvs_p": null,
"transcript": "XR_007063069.1",
"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": 1663,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC39A5",
"gene_hgnc_id": 20502,
"dbsnp": "rs587777625",
"frequency_reference_population": 6.840928e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84093e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5827420949935913,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.288,
"revel_prediction": "Benign",
"alphamissense_score": 0.2393,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.037,
"phylop100way_prediction": "Benign",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PM5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000454355.7",
"gene_symbol": "SLC39A5",
"hgnc_id": 20502,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.911T>G",
"hgvs_p": "p.Met304Arg"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}