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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: 19-2732984-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=2732984&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 2732984,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_144564.5",
"consequences": [
{
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "NM_144564.5",
"protein_id": "NP_653165.2",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000269740.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144564.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000269740.9",
"protein_id": "ENSP00000269740.3",
"transcript_support_level": 1,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_144564.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000269740.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000267001",
"gene_hgnc_id": null,
"hgvs_c": "c.210+4064G>A",
"hgvs_p": null,
"transcript": "ENST00000586572.1",
"protein_id": "ENSP00000467958.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 104,
"cds_start": null,
"cds_end": null,
"cds_length": 317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000586572.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000545664.5",
"protein_id": "ENSP00000445345.1",
"transcript_support_level": 2,
"aa_start": 238,
"aa_end": null,
"aa_length": 323,
"cds_start": 712,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000545664.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000909979.1",
"protein_id": "ENSP00000580038.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909979.1"
},
{
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000909980.1",
"protein_id": "ENSP00000580039.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909980.1"
},
{
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000909981.1",
"protein_id": "ENSP00000580040.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909981.1"
},
{
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000909982.1",
"protein_id": "ENSP00000580041.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909982.1"
},
{
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000959861.1",
"protein_id": "ENSP00000629920.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959861.1"
},
{
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000959862.1",
"protein_id": "ENSP00000629921.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959862.1"
},
{
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr",
"transcript": "ENST00000959863.1",
"protein_id": "ENSP00000629922.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 314,
"cds_start": 712,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959863.1"
},
{
"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": "SLC39A3",
"gene_hgnc_id": 17128,
"hgvs_c": "c.706G>A",
"hgvs_p": "p.Ala236Thr",
"transcript": "ENST00000909983.1",
"protein_id": "ENSP00000580042.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 312,
"cds_start": 706,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909983.1"
}
],
"gene_symbol": "SLC39A3",
"gene_hgnc_id": 17128,
"dbsnp": "rs150805133",
"frequency_reference_population": 0.000033745277,
"hom_count_reference_population": 0,
"allele_count_reference_population": 54,
"gnomad_exomes_af": 0.0000331493,
"gnomad_genomes_af": 0.0000394146,
"gnomad_exomes_ac": 48,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11777496337890625,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.116,
"revel_prediction": "Benign",
"alphamissense_score": 0.0869,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.036,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_144564.5",
"gene_symbol": "SLC39A3",
"hgnc_id": 17128,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.712G>A",
"hgvs_p": "p.Ala238Thr"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000586572.1",
"gene_symbol": "ENSG00000267001",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.210+4064G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}