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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: 13-48077193-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=48077193&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 48077193,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000258648.7",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED4",
"gene_hgnc_id": 17903,
"hgvs_c": "c.759T>A",
"hgvs_p": "p.Asp253Glu",
"transcript": "NM_014166.4",
"protein_id": "NP_054885.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 270,
"cds_start": 759,
"cds_end": null,
"cds_length": 813,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 2254,
"mane_select": "ENST00000258648.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED4",
"gene_hgnc_id": 17903,
"hgvs_c": "c.759T>A",
"hgvs_p": "p.Asp253Glu",
"transcript": "ENST00000258648.7",
"protein_id": "ENSP00000258648.2",
"transcript_support_level": 1,
"aa_start": 253,
"aa_end": null,
"aa_length": 270,
"cds_start": 759,
"cds_end": null,
"cds_length": 813,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 2254,
"mane_select": "NM_014166.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED4",
"gene_hgnc_id": 17903,
"hgvs_c": "c.693T>A",
"hgvs_p": "p.Asp231Glu",
"transcript": "ENST00000417167.2",
"protein_id": "ENSP00000413595.1",
"transcript_support_level": 5,
"aa_start": 231,
"aa_end": null,
"aa_length": 237,
"cds_start": 693,
"cds_end": null,
"cds_length": 715,
"cdna_start": 889,
"cdna_end": null,
"cdna_length": 911,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED4",
"gene_hgnc_id": 17903,
"hgvs_c": "c.621T>A",
"hgvs_p": "p.Asp207Glu",
"transcript": "NM_001270629.2",
"protein_id": "NP_001257558.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 224,
"cds_start": 621,
"cds_end": null,
"cds_length": 675,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 2148,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED4",
"gene_hgnc_id": 17903,
"hgvs_c": "c.621T>A",
"hgvs_p": "p.Asp207Glu",
"transcript": "ENST00000378586.5",
"protein_id": "ENSP00000367849.1",
"transcript_support_level": 2,
"aa_start": 207,
"aa_end": null,
"aa_length": 224,
"cds_start": 621,
"cds_end": null,
"cds_length": 675,
"cdna_start": 706,
"cdna_end": null,
"cdna_length": 931,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED4-AS1",
"gene_hgnc_id": 39213,
"hgvs_c": "n.57A>T",
"hgvs_p": null,
"transcript": "ENST00000422483.1",
"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": 542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED4",
"gene_hgnc_id": 17903,
"hgvs_c": "n.249T>A",
"hgvs_p": null,
"transcript": "ENST00000495013.5",
"protein_id": "ENSP00000483651.1",
"transcript_support_level": 3,
"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": 460,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED4-AS1",
"gene_hgnc_id": 39213,
"hgvs_c": "n.57A>T",
"hgvs_p": null,
"transcript": "NR_046511.1",
"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": 544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MED4-AS1",
"gene_hgnc_id": 39213,
"hgvs_c": "n.375-26A>T",
"hgvs_p": null,
"transcript": "ENST00000844353.1",
"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": 853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MED4",
"gene_hgnc_id": 17903,
"dbsnp": "rs146226547",
"frequency_reference_population": 0.0025595985,
"hom_count_reference_population": 16,
"allele_count_reference_population": 4118,
"gnomad_exomes_af": 0.00251346,
"gnomad_genomes_af": 0.00300093,
"gnomad_exomes_ac": 3661,
"gnomad_genomes_ac": 457,
"gnomad_exomes_homalt": 15,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008309990167617798,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.171,
"revel_prediction": "Benign",
"alphamissense_score": 0.1927,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.823,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000258648.7",
"gene_symbol": "MED4",
"hgnc_id": 17903,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.759T>A",
"hgvs_p": "p.Asp253Glu"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000422483.1",
"gene_symbol": "MED4-AS1",
"hgnc_id": 39213,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.57A>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}