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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: 19-13768642-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=13768642&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 13768642,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000040663.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "c.629G>A",
"hgvs_p": "p.Arg210Gln",
"transcript": "NM_001031727.4",
"protein_id": "NP_001026897.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 369,
"cds_start": 629,
"cds_end": null,
"cds_length": 1110,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 3178,
"mane_select": "ENST00000040663.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "c.629G>A",
"hgvs_p": "p.Arg210Gln",
"transcript": "ENST00000040663.8",
"protein_id": "ENSP00000040663.5",
"transcript_support_level": 1,
"aa_start": 210,
"aa_end": null,
"aa_length": 369,
"cds_start": 629,
"cds_end": null,
"cds_length": 1110,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 3178,
"mane_select": "NM_001031727.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "c.488G>A",
"hgvs_p": "p.Arg163Gln",
"transcript": "ENST00000319545.12",
"protein_id": "ENSP00000314871.7",
"transcript_support_level": 1,
"aa_start": 163,
"aa_end": null,
"aa_length": 322,
"cds_start": 488,
"cds_end": null,
"cds_length": 969,
"cdna_start": 545,
"cdna_end": null,
"cdna_length": 3027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "c.542G>A",
"hgvs_p": "p.Arg181Gln",
"transcript": "NM_001329572.2",
"protein_id": "NP_001316501.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 340,
"cds_start": 542,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 609,
"cdna_end": null,
"cdna_length": 3091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "c.488G>A",
"hgvs_p": "p.Arg163Gln",
"transcript": "NM_032285.4",
"protein_id": "NP_115661.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 322,
"cds_start": 488,
"cds_end": null,
"cds_length": 969,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 3037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "c.629G>A",
"hgvs_p": "p.Arg210Gln",
"transcript": "XM_011528356.3",
"protein_id": "XP_011526658.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 322,
"cds_start": 629,
"cds_end": null,
"cds_length": 969,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 3321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "c.140G>A",
"hgvs_p": "p.Arg47Gln",
"transcript": "XM_047439509.1",
"protein_id": "XP_047295465.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 206,
"cds_start": 140,
"cds_end": null,
"cds_length": 621,
"cdna_start": 241,
"cdna_end": null,
"cdna_length": 2723,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "n.824G>A",
"hgvs_p": null,
"transcript": "ENST00000588526.5",
"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": 862,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "n.669G>A",
"hgvs_p": null,
"transcript": "ENST00000591688.5",
"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": 897,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "n.721G>A",
"hgvs_p": null,
"transcript": "NR_138051.2",
"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": 3203,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "n.898G>A",
"hgvs_p": null,
"transcript": "XR_244089.5",
"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": 1105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "c.*76G>A",
"hgvs_p": null,
"transcript": "XM_011528357.4",
"protein_id": "XP_011526659.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 213,
"cds_start": -4,
"cds_end": null,
"cds_length": 642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 797,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "n.*61G>A",
"hgvs_p": null,
"transcript": "ENST00000589290.1",
"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": 602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"hgvs_c": "n.*85G>A",
"hgvs_p": null,
"transcript": "ENST00000593245.5",
"protein_id": null,
"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": 786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MRI1",
"gene_hgnc_id": 28469,
"dbsnp": "rs141094096",
"frequency_reference_population": 0.00009976589,
"hom_count_reference_population": 1,
"allele_count_reference_population": 161,
"gnomad_exomes_af": 0.000100585,
"gnomad_genomes_af": 0.0000919081,
"gnomad_exomes_ac": 147,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7941559553146362,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.959,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4147,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.939,
"phylop100way_prediction": "Pathogenic",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000040663.8",
"gene_symbol": "MRI1",
"hgnc_id": 28469,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.629G>A",
"hgvs_p": "p.Arg210Gln"
}
],
"clinvar_disease": "Infantile epilepsy,Severe cystic degeneration of the brain,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Severe cystic degeneration of the brain;Infantile epilepsy|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}