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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: 16-3050094-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=3050094&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 3050094,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000336577.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"hgvs_c": "c.318C>T",
"hgvs_p": "p.Arg106Arg",
"transcript": "NM_022468.5",
"protein_id": "NP_071913.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 562,
"cds_start": 318,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 675,
"cdna_end": null,
"cdna_length": 3674,
"mane_select": "ENST00000336577.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"hgvs_c": "c.318C>T",
"hgvs_p": "p.Arg106Arg",
"transcript": "ENST00000336577.9",
"protein_id": "ENSP00000337816.4",
"transcript_support_level": 1,
"aa_start": 106,
"aa_end": null,
"aa_length": 562,
"cds_start": 318,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 675,
"cdna_end": null,
"cdna_length": 3674,
"mane_select": "NM_022468.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"hgvs_c": "c.318C>T",
"hgvs_p": "p.Arg106Arg",
"transcript": "ENST00000850602.1",
"protein_id": "ENSP00000520889.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 562,
"cds_start": 318,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 675,
"cdna_end": null,
"cdna_length": 3677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"hgvs_c": "c.216C>T",
"hgvs_p": "p.Arg72Arg",
"transcript": "XM_024450391.2",
"protein_id": "XP_024306159.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 528,
"cds_start": 216,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 572,
"cdna_end": null,
"cdna_length": 3571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"hgvs_c": "c.318C>T",
"hgvs_p": "p.Arg106Arg",
"transcript": "XM_017023561.2",
"protein_id": "XP_016879050.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 287,
"cds_start": 318,
"cds_end": null,
"cds_length": 864,
"cdna_start": 675,
"cdna_end": null,
"cdna_length": 1221,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"hgvs_c": "n.103C>T",
"hgvs_p": null,
"transcript": "ENST00000570755.1",
"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": 779,
"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": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"hgvs_c": "n.318C>T",
"hgvs_p": null,
"transcript": "ENST00000612971.2",
"protein_id": "ENSP00000482854.2",
"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": 4413,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "MMP25-AS1",
"gene_hgnc_id": 51372,
"hgvs_c": "n.1110+1566G>A",
"hgvs_p": null,
"transcript": "ENST00000576250.6",
"protein_id": null,
"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": 1974,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MMP25-AS1",
"gene_hgnc_id": 51372,
"hgvs_c": "n.2174+1566G>A",
"hgvs_p": null,
"transcript": "ENST00000649784.1",
"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": 3263,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"hgvs_c": "c.232+2547C>T",
"hgvs_p": null,
"transcript": "XM_024450390.2",
"protein_id": "XP_024306158.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 419,
"cds_start": -4,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MMP25",
"gene_hgnc_id": 14246,
"dbsnp": "rs10431961",
"frequency_reference_population": 0.3228306,
"hom_count_reference_population": 86150,
"allele_count_reference_population": 520062,
"gnomad_exomes_af": 0.326464,
"gnomad_genomes_af": 0.287991,
"gnomad_exomes_ac": 476247,
"gnomad_genomes_ac": 43815,
"gnomad_exomes_homalt": 79445,
"gnomad_genomes_homalt": 6705,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.354,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000336577.9",
"gene_symbol": "MMP25",
"hgnc_id": 14246,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.318C>T",
"hgvs_p": "p.Arg106Arg"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000649784.1",
"gene_symbol": "MMP25-AS1",
"hgnc_id": 51372,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2174+1566G>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
}