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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: 5-149981067-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=149981067&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 149981067,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000286298.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492Trp",
"transcript": "NM_000112.4",
"protein_id": "NP_000103.2",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 739,
"cds_start": 1474,
"cds_end": null,
"cds_length": 2220,
"cdna_start": 1721,
"cdna_end": null,
"cdna_length": 8054,
"mane_select": "ENST00000286298.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492Trp",
"transcript": "ENST00000286298.5",
"protein_id": "ENSP00000286298.4",
"transcript_support_level": 1,
"aa_start": 492,
"aa_end": null,
"aa_length": 739,
"cds_start": 1474,
"cds_end": null,
"cds_length": 2220,
"cdna_start": 1721,
"cdna_end": null,
"cdna_length": 8054,
"mane_select": "NM_000112.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492Trp",
"transcript": "XM_017009191.3",
"protein_id": "XP_016864680.1",
"transcript_support_level": null,
"aa_start": 492,
"aa_end": null,
"aa_length": 739,
"cds_start": 1474,
"cds_end": null,
"cds_length": 2220,
"cdna_start": 1721,
"cdna_end": null,
"cdna_length": 7951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"hgvs_c": "c.372+2716C>T",
"hgvs_p": null,
"transcript": "ENST00000503336.1",
"protein_id": "ENSP00000426053.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 124,
"cds_start": -4,
"cds_end": null,
"cds_length": 375,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC26A2",
"gene_hgnc_id": 10994,
"dbsnp": "rs78676079",
"frequency_reference_population": 0.02071944,
"hom_count_reference_population": 428,
"allele_count_reference_population": 33443,
"gnomad_exomes_af": 0.0212325,
"gnomad_genomes_af": 0.0157943,
"gnomad_exomes_ac": 31038,
"gnomad_genomes_ac": 2405,
"gnomad_exomes_homalt": 402,
"gnomad_genomes_homalt": 26,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.014791309833526611,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.671,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2115,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.512,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000286298.5",
"gene_symbol": "SLC26A2",
"hgnc_id": 10994,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1474C>T",
"hgvs_p": "p.Arg492Trp"
}
],
"clinvar_disease": " type IB,Achondrogenesis,Atelosteogenesis type II,Connective tissue disorder,Diastrophic dysplasia,Multiple epiphyseal dysplasia type 4,Sulfate transporter-related osteochondrodysplasia,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:10 O:1",
"phenotype_combined": "Diastrophic dysplasia|Achondrogenesis, type IB|Multiple epiphyseal dysplasia type 4|not specified|Atelosteogenesis type II|Sulfate transporter-related osteochondrodysplasia|Achondrogenesis, type IB;Diastrophic dysplasia;Atelosteogenesis type II;Multiple epiphyseal dysplasia type 4|not provided|Connective tissue disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}