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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: 19-39397581-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=39397581&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 39397581,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_017592.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "c.485C>T",
"hgvs_p": "p.Ala162Val",
"transcript": "NM_017592.4",
"protein_id": "NP_060062.2",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 200,
"cds_start": 485,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000315588.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017592.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "c.485C>T",
"hgvs_p": "p.Ala162Val",
"transcript": "ENST00000315588.11",
"protein_id": "ENSP00000314343.5",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 200,
"cds_start": 485,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017592.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000315588.11"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "c.548C>T",
"hgvs_p": "p.Ala183Val",
"transcript": "ENST00000615911.4",
"protein_id": "ENSP00000481733.1",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 221,
"cds_start": 548,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000615911.4"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "c.508C>T",
"hgvs_p": "p.Arg170Trp",
"transcript": "ENST00000596297.1",
"protein_id": "ENSP00000473181.2",
"transcript_support_level": 5,
"aa_start": 170,
"aa_end": null,
"aa_length": 207,
"cds_start": 508,
"cds_end": null,
"cds_length": 625,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596297.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "c.415C>T",
"hgvs_p": "p.Arg139Trp",
"transcript": "NM_001317770.3",
"protein_id": "NP_001304699.2",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 196,
"cds_start": 415,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001317770.3"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "c.415C>T",
"hgvs_p": "p.Arg139Trp",
"transcript": "ENST00000594368.5",
"protein_id": "ENSP00000472501.2",
"transcript_support_level": 2,
"aa_start": 139,
"aa_end": null,
"aa_length": 196,
"cds_start": 415,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000594368.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"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": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "c.422C>T",
"hgvs_p": "p.Ala141Val",
"transcript": "ENST00000865179.1",
"protein_id": "ENSP00000535238.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 179,
"cds_start": 422,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865179.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "c.341C>T",
"hgvs_p": "p.Ala114Val",
"transcript": "ENST00000865180.1",
"protein_id": "ENSP00000535239.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 152,
"cds_start": 341,
"cds_end": null,
"cds_length": 459,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865180.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "n.*198C>T",
"hgvs_p": null,
"transcript": "ENST00000599417.2",
"protein_id": "ENSP00000471101.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000599417.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "n.471C>T",
"hgvs_p": null,
"transcript": "NR_133915.3",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_133915.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"hgvs_c": "n.*198C>T",
"hgvs_p": null,
"transcript": "ENST00000599417.2",
"protein_id": "ENSP00000471101.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000599417.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307007",
"gene_hgnc_id": null,
"hgvs_c": "n.118+5333G>A",
"hgvs_p": null,
"transcript": "ENST00000822559.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000822559.1"
}
],
"gene_symbol": "MED29",
"gene_hgnc_id": 23074,
"dbsnp": "rs777845155",
"frequency_reference_population": 0.000004105697,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.0000041057,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23688921332359314,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.051,
"revel_prediction": "Benign",
"alphamissense_score": 0.3626,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.579,
"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_017592.4",
"gene_symbol": "MED29",
"hgnc_id": 23074,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.485C>T",
"hgvs_p": "p.Ala162Val"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000822559.1",
"gene_symbol": "ENSG00000307007",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.118+5333G>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
}