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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: 19-15109997-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=15109997&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 15109997,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_033025.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Pro242Ser",
"transcript": "NM_033025.6",
"protein_id": "NP_149014.3",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 735,
"cds_start": 724,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000342784.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_033025.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Pro242Ser",
"transcript": "ENST00000342784.7",
"protein_id": "ENSP00000341489.1",
"transcript_support_level": 2,
"aa_start": 242,
"aa_end": null,
"aa_length": 735,
"cds_start": 724,
"cds_end": null,
"cds_length": 2208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_033025.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342784.7"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.523C>T",
"hgvs_p": "p.Pro175Ser",
"transcript": "ENST00000600440.5",
"protein_id": "ENSP00000470733.1",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 668,
"cds_start": 523,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600440.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Pro242Ser",
"transcript": "ENST00000863344.1",
"protein_id": "ENSP00000533403.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 756,
"cds_start": 724,
"cds_end": null,
"cds_length": 2271,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863344.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Pro242Ser",
"transcript": "ENST00000863343.1",
"protein_id": "ENSP00000533402.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 741,
"cds_start": 724,
"cds_end": null,
"cds_length": 2226,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863343.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.523C>T",
"hgvs_p": "p.Pro175Ser",
"transcript": "NM_001300910.2",
"protein_id": "NP_001287839.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 668,
"cds_start": 523,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001300910.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.382C>T",
"hgvs_p": "p.Pro128Ser",
"transcript": "ENST00000863345.1",
"protein_id": "ENSP00000533404.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 621,
"cds_start": 382,
"cds_end": null,
"cds_length": 1866,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863345.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.1030C>T",
"hgvs_p": "p.Pro344Ser",
"transcript": "XM_047439579.1",
"protein_id": "XP_047295535.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 837,
"cds_start": 1030,
"cds_end": null,
"cds_length": 2514,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439579.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.1030C>T",
"hgvs_p": "p.Pro344Ser",
"transcript": "XM_047439580.1",
"protein_id": "XP_047295536.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 729,
"cds_start": 1030,
"cds_end": null,
"cds_length": 2190,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439580.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Pro242Ser",
"transcript": "XM_024451750.2",
"protein_id": "XP_024307518.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 627,
"cds_start": 724,
"cds_end": null,
"cds_length": 1884,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024451750.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.523C>T",
"hgvs_p": "p.Pro175Ser",
"transcript": "XM_047439581.1",
"protein_id": "XP_047295537.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 560,
"cds_start": 523,
"cds_end": null,
"cds_length": 1683,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047439581.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.-478C>T",
"hgvs_p": null,
"transcript": "ENST00000600252.5",
"protein_id": "ENSP00000469489.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 392,
"cds_start": null,
"cds_end": null,
"cds_length": 1179,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600252.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"hgvs_c": "c.89-524C>T",
"hgvs_p": null,
"transcript": "ENST00000925189.1",
"protein_id": "ENSP00000595248.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 406,
"cds_start": null,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925189.1"
}
],
"gene_symbol": "SYDE1",
"gene_hgnc_id": 25824,
"dbsnp": "rs1415453980",
"frequency_reference_population": 0.0000013384641,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 7.4508e-7,
"gnomad_genomes_af": 0.0000065741,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07606148719787598,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.064,
"revel_prediction": "Benign",
"alphamissense_score": 0.0887,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.188,
"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": 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_033025.6",
"gene_symbol": "SYDE1",
"hgnc_id": 25824,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Pro242Ser"
}
],
"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
}