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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: 5-149960981-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=149960981&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 149960981,
"ref": "T",
"alt": "C",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000286298.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "c.-26+2T>C",
"hgvs_p": null,
"transcript": "NM_000112.4",
"protein_id": "NP_000103.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 739,
"cds_start": -4,
"cds_end": null,
"cds_length": 2220,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8054,
"mane_select": "ENST00000286298.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "c.-26+2T>C",
"hgvs_p": null,
"transcript": "ENST00000286298.5",
"protein_id": "ENSP00000286298.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 739,
"cds_start": -4,
"cds_end": null,
"cds_length": 2220,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8054,
"mane_select": "NM_000112.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "c.-306+2T>C",
"hgvs_p": null,
"transcript": "ENST00000433184.1",
"protein_id": "ENSP00000405496.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 22,
"cds_start": -4,
"cds_end": null,
"cds_length": 70,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "n.207+2T>C",
"hgvs_p": null,
"transcript": "ENST00000690410.1",
"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": 2557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "c.-26+2T>C",
"hgvs_p": null,
"transcript": "XM_017009191.3",
"protein_id": "XP_016864680.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 739,
"cds_start": -4,
"cds_end": null,
"cds_length": 2220,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"dbsnp": "rs386833492",
"frequency_reference_population": 0.0005411041,
"hom_count_reference_population": 0,
"allele_count_reference_population": 82,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.000541104,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 82,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.009999999776482582,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8560000061988831,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.993,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.9,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999907736518652,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000286298.5",
"gene_symbol": "SLC26A2",
"hgnc_id": 10994,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-26+2T>C",
"hgvs_p": null
}
],
"clinvar_disease": " type IB,3MC syndrome 2,Achondrogenesis,Atelosteogenesis type II,Diastrophic dysplasia,Multiple epiphyseal dysplasia type 4,SLC26A2-related disorder,Sulfate transporter-related osteochondrodysplasia,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:17 O:1",
"phenotype_combined": "Diastrophic dysplasia|Achondrogenesis, type IB;Multiple epiphyseal dysplasia type 4;Atelosteogenesis type II;Diastrophic dysplasia|Multiple epiphyseal dysplasia type 4|not provided|Sulfate transporter-related osteochondrodysplasia|SLC26A2-related disorder|3MC syndrome 2|Atelosteogenesis type II|Achondrogenesis, type IB",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}