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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: 1-240493438-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=240493438&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PP2",
"PP5",
"BP4",
"BS2_Supporting"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GREM2",
"hgnc_id": 17655,
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_022469.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2,PP5,BP4,BS2_Supporting",
"acmg_score": 0,
"allele_count_reference_population": 79,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0836,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " 9, selective,Tooth agenesis",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.010894209146499634,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 168,
"aa_ref": "A",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4176,
"cdna_start": 311,
"cds_end": null,
"cds_length": 507,
"cds_start": 38,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_022469.4",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000318160.5",
"protein_coding": true,
"protein_id": "NP_071914.3",
"strand": false,
"transcript": "NM_022469.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 168,
"aa_ref": "A",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4176,
"cdna_start": 311,
"cds_end": null,
"cds_length": 507,
"cds_start": 38,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000318160.5",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_022469.4",
"protein_coding": true,
"protein_id": "ENSP00000318650.4",
"strand": false,
"transcript": "ENST00000318160.5",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 168,
"aa_ref": "A",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3368,
"cdna_start": 431,
"cds_end": null,
"cds_length": 507,
"cds_start": 38,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000859904.1",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000529963.1",
"strand": false,
"transcript": "ENST00000859904.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 168,
"aa_ref": "A",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3944,
"cdna_start": 81,
"cds_end": null,
"cds_length": 507,
"cds_start": 38,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000859905.1",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000529964.1",
"strand": false,
"transcript": "ENST00000859905.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 168,
"aa_ref": "A",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1541,
"cdna_start": 125,
"cds_end": null,
"cds_length": 507,
"cds_start": 38,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000859906.1",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000529965.1",
"strand": false,
"transcript": "ENST00000859906.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 168,
"aa_ref": "A",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1831,
"cdna_start": 129,
"cds_end": null,
"cds_length": 507,
"cds_start": 38,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000942417.1",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612476.1",
"strand": false,
"transcript": "ENST00000942417.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 186,
"aa_ref": "A",
"aa_start": 31,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4505,
"cdna_start": 640,
"cds_end": null,
"cds_length": 561,
"cds_start": 92,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047427832.1",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.92C>T",
"hgvs_p": "p.Ala31Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283788.1",
"strand": false,
"transcript": "XM_047427832.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 186,
"aa_ref": "A",
"aa_start": 31,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4594,
"cdna_start": 729,
"cds_end": null,
"cds_length": 561,
"cds_start": 92,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047427839.1",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.92C>T",
"hgvs_p": "p.Ala31Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283795.1",
"strand": false,
"transcript": "XM_047427839.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 168,
"aa_ref": "A",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4296,
"cdna_start": 431,
"cds_end": null,
"cds_length": 507,
"cds_start": 38,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_011544249.3",
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"hgvs_c": "c.38C>T",
"hgvs_p": "p.Ala13Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011542551.1",
"strand": false,
"transcript": "XM_011544249.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs373941682",
"effect": "missense_variant",
"frequency_reference_population": 0.00004904584,
"gene_hgnc_id": 17655,
"gene_symbol": "GREM2",
"gnomad_exomes_ac": 63,
"gnomad_exomes_af": 0.0000431977,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 16,
"gnomad_genomes_af": 0.000105037,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Tooth agenesis, selective, 9",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.93,
"pos": 240493438,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.031,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_022469.4"
}
]
}