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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: 14-46957454-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=46957454&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 46957454,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001113498.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.2009T>C",
"hgvs_p": "p.Leu670Pro",
"transcript": "NM_001113498.3",
"protein_id": "NP_001106970.4",
"transcript_support_level": null,
"aa_start": 670,
"aa_end": null,
"aa_length": 1025,
"cds_start": 2009,
"cds_end": null,
"cds_length": 3078,
"cdna_start": 2818,
"cdna_end": null,
"cdna_length": 5726,
"mane_select": "ENST00000399232.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.2009T>C",
"hgvs_p": "p.Leu670Pro",
"transcript": "ENST00000399232.8",
"protein_id": "ENSP00000382178.4",
"transcript_support_level": 1,
"aa_start": 670,
"aa_end": null,
"aa_length": 1025,
"cds_start": 2009,
"cds_end": null,
"cds_length": 3078,
"cdna_start": 2818,
"cdna_end": null,
"cdna_length": 5726,
"mane_select": "NM_001113498.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.1115T>C",
"hgvs_p": "p.Leu372Pro",
"transcript": "NM_182830.4",
"protein_id": "NP_878250.2",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 727,
"cds_start": 1115,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 5250,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.1115T>C",
"hgvs_p": "p.Leu372Pro",
"transcript": "ENST00000357362.7",
"protein_id": "ENSP00000349925.3",
"transcript_support_level": 5,
"aa_start": 372,
"aa_end": null,
"aa_length": 727,
"cds_start": 1115,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 1750,
"cdna_end": null,
"cdna_length": 2965,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.1874T>C",
"hgvs_p": "p.Leu625Pro",
"transcript": "XM_011536519.3",
"protein_id": "XP_011534821.1",
"transcript_support_level": null,
"aa_start": 625,
"aa_end": null,
"aa_length": 980,
"cds_start": 1874,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 6933,
"cdna_end": null,
"cdna_length": 10310,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.1115T>C",
"hgvs_p": "p.Leu372Pro",
"transcript": "XM_047431048.1",
"protein_id": "XP_047287004.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 727,
"cds_start": 1115,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 1878,
"cdna_end": null,
"cdna_length": 5255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.1115T>C",
"hgvs_p": "p.Leu372Pro",
"transcript": "XM_047431049.1",
"protein_id": "XP_047287005.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 727,
"cds_start": 1115,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 1944,
"cdna_end": null,
"cdna_length": 5321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.1115T>C",
"hgvs_p": "p.Leu372Pro",
"transcript": "XM_047431050.1",
"protein_id": "XP_047287006.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 727,
"cds_start": 1115,
"cds_end": null,
"cds_length": 2184,
"cdna_start": 1786,
"cdna_end": null,
"cdna_length": 5163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.647T>C",
"hgvs_p": "p.Leu216Pro",
"transcript": "XM_017021060.2",
"protein_id": "XP_016876549.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 571,
"cds_start": 647,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 1133,
"cdna_end": null,
"cdna_length": 4510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.482T>C",
"hgvs_p": "p.Leu161Pro",
"transcript": "XM_011536525.3",
"protein_id": "XP_011534827.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 516,
"cds_start": 482,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 3955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "n.*387T>C",
"hgvs_p": null,
"transcript": "ENST00000557238.5",
"protein_id": "ENSP00000452593.1",
"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": 3635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "n.*387T>C",
"hgvs_p": null,
"transcript": "ENST00000557238.5",
"protein_id": "ENSP00000452593.1",
"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": 3635,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"hgvs_c": "c.*227T>C",
"hgvs_p": null,
"transcript": "XM_011536522.4",
"protein_id": "XP_011534824.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 621,
"cds_start": -4,
"cds_end": null,
"cds_length": 1866,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MDGA2",
"gene_hgnc_id": 19835,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6798547506332397,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.43,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.6487,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.638,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001113498.3",
"gene_symbol": "MDGA2",
"hgnc_id": 19835,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2009T>C",
"hgvs_p": "p.Leu670Pro"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}