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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: 6-31743191-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31743191&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 31743191,
"ref": "T",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000493662.6",
"consequences": [
{
"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": 25,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "NM_172166.4",
"protein_id": "NP_751898.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 834,
"cds_start": -4,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": "ENST00000375750.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "ENST00000375750.9",
"protein_id": "ENSP00000364903.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 834,
"cds_start": -4,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": "NM_172166.4",
"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": 25,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "ENST00000375703.7",
"protein_id": "ENSP00000364855.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 835,
"cds_start": -4,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2708,
"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": 25,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "ENST00000375755.8",
"protein_id": "ENSP00000364908.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 834,
"cds_start": -4,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2936,
"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": 25,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "ENST00000375740.7",
"protein_id": "ENSP00000364892.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 822,
"cds_start": -4,
"cds_end": null,
"cds_length": 2469,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5-SAPCD1",
"gene_hgnc_id": 41994,
"hgvs_c": "n.415+21T>A",
"hgvs_p": null,
"transcript": "ENST00000493662.6",
"protein_id": "ENSP00000417871.2",
"transcript_support_level": 1,
"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": 3991,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.507T>A",
"hgvs_p": null,
"transcript": "ENST00000463094.5",
"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": 796,
"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": 25,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "NM_172165.4",
"protein_id": "NP_751897.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 835,
"cds_start": -4,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2724,
"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": 25,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "NM_002441.5",
"protein_id": "NP_002432.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 834,
"cds_start": -4,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2879,
"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": 25,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "NM_025259.6",
"protein_id": "NP_079535.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 822,
"cds_start": -4,
"cds_end": null,
"cds_length": 2469,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2685,
"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": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.415+21T>A",
"hgvs_p": null,
"transcript": "ENST00000425703.5",
"protein_id": "ENSP00000402842.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": -4,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 694,
"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": 24,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.415+21T>A",
"hgvs_p": null,
"transcript": "ENST00000423982.6",
"protein_id": "ENSP00000406352.2",
"transcript_support_level": 5,
"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": 2706,
"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": 22,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.184+21T>A",
"hgvs_p": null,
"transcript": "ENST00000463144.5",
"protein_id": "ENSP00000419648.1",
"transcript_support_level": 5,
"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": 2296,
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.486+21T>A",
"hgvs_p": null,
"transcript": "ENST00000482280.1",
"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": 944,
"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": 20,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.639+21T>A",
"hgvs_p": null,
"transcript": "ENST00000650702.1",
"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": 3053,
"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": 29,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MSH5-SAPCD1",
"gene_hgnc_id": 41994,
"hgvs_c": "n.543+21T>A",
"hgvs_p": null,
"transcript": "NR_037846.1",
"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": 4063,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.*42T>A",
"hgvs_p": null,
"transcript": "ENST00000652715.1",
"protein_id": "ENSP00000498591.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 130,
"cds_start": -4,
"cds_end": null,
"cds_length": 394,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MSH5-SAPCD1",
"gene_hgnc_id": 41994,
"dbsnp": "rs707915",
"frequency_reference_population": 0.07117655,
"hom_count_reference_population": 5250,
"allele_count_reference_population": 114665,
"gnomad_exomes_af": 0.0673655,
"gnomad_genomes_af": 0.107727,
"gnomad_exomes_ac": 98278,
"gnomad_genomes_ac": 16387,
"gnomad_exomes_homalt": 4046,
"gnomad_genomes_homalt": 1204,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7300000190734863,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.501,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000493662.6",
"gene_symbol": "MSH5-SAPCD1",
"hgnc_id": 41994,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.415+21T>A",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000375750.9",
"gene_symbol": "MSH5",
"hgnc_id": 7328,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.415+21T>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}