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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: 2-47678251-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=47678251&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 47678251,
"ref": "C",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_001406633.1",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2897C>A",
"hgvs_p": "p.Pro966His",
"transcript": "NM_001406633.1",
"protein_id": "NP_001393562.1",
"transcript_support_level": null,
"aa_start": 966,
"aa_end": null,
"aa_length": 975,
"cds_start": 2897,
"cds_end": null,
"cds_length": 2928,
"cdna_start": 2933,
"cdna_end": null,
"cdna_length": 3134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "n.3099C>A",
"hgvs_p": null,
"transcript": "NR_176241.1",
"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": 3300,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "n.2895C>A",
"hgvs_p": null,
"transcript": "NR_176243.1",
"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": 3096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "n.3525C>A",
"hgvs_p": null,
"transcript": "NR_176244.1",
"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": 3726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "n.2981C>A",
"hgvs_p": null,
"transcript": "NR_176245.1",
"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": 3182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "n.3007C>A",
"hgvs_p": null,
"transcript": "NR_176247.1",
"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": 3208,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "n.3207C>A",
"hgvs_p": null,
"transcript": "NR_176248.1",
"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": 3408,
"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": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2895-849C>A",
"hgvs_p": null,
"transcript": "NM_001406635.1",
"protein_id": "NP_001393564.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 969,
"cds_start": -4,
"cds_end": null,
"cds_length": 2910,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3051,
"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": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2862-849C>A",
"hgvs_p": null,
"transcript": "NM_001406636.1",
"protein_id": "NP_001393565.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 958,
"cds_start": -4,
"cds_end": null,
"cds_length": 2877,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3018,
"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": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2753-29932C>A",
"hgvs_p": null,
"transcript": "NM_001406637.1",
"protein_id": "NP_001393566.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 957,
"cds_start": -4,
"cds_end": null,
"cds_length": 2874,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4436,
"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": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.*38-849C>A",
"hgvs_p": null,
"transcript": "NM_001406640.1",
"protein_id": "NP_001393569.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 945,
"cds_start": -4,
"cds_end": null,
"cds_length": 2838,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3032,
"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": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "c.2753-849C>A",
"hgvs_p": null,
"transcript": "NM_001406642.1",
"protein_id": "NP_001393571.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 929,
"cds_start": -4,
"cds_end": null,
"cds_length": 2790,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2909,
"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": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "n.3112-849C>A",
"hgvs_p": null,
"transcript": "NR_176242.1",
"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": 3232,
"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": 19,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"hgvs_c": "n.3144-849C>A",
"hgvs_p": null,
"transcript": "NR_176246.1",
"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": 3264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MSH2",
"gene_hgnc_id": 7325,
"dbsnp": "rs17036817",
"frequency_reference_population": 0.039079856,
"hom_count_reference_population": 965,
"allele_count_reference_population": 17838,
"gnomad_exomes_af": 0.0409297,
"gnomad_genomes_af": 0.03538,
"gnomad_exomes_ac": 12455,
"gnomad_genomes_ac": 5383,
"gnomad_exomes_homalt": 690,
"gnomad_genomes_homalt": 275,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9100000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.91,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.295,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"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": "NM_001406633.1",
"gene_symbol": "MSH2",
"hgnc_id": 7325,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2897C>A",
"hgvs_p": "p.Pro966His"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "not provided",
"clinvar_review_status": "no classification provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "not provided",
"custom_annotations": null
}
],
"message": null
}