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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: 19-41999254-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41999254&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41999254,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002088.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.2560T>A",
"hgvs_p": "p.Ser854Thr",
"transcript": "NM_002088.5",
"protein_id": "NP_002079.3",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 980,
"cds_start": 2560,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 3576,
"cdna_end": null,
"cdna_length": 4506,
"mane_select": "ENST00000593562.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002088.5"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.2560T>A",
"hgvs_p": "p.Ser854Thr",
"transcript": "ENST00000593562.6",
"protein_id": "ENSP00000470251.1",
"transcript_support_level": 5,
"aa_start": 854,
"aa_end": null,
"aa_length": 980,
"cds_start": 2560,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 3576,
"cdna_end": null,
"cdna_length": 4506,
"mane_select": "NM_002088.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000593562.6"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.2560T>A",
"hgvs_p": "p.Ser854Thr",
"transcript": "ENST00000262895.7",
"protein_id": "ENSP00000262895.2",
"transcript_support_level": 1,
"aa_start": 854,
"aa_end": null,
"aa_length": 980,
"cds_start": 2560,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2560,
"cdna_end": null,
"cdna_length": 3493,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262895.7"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "n.1437T>A",
"hgvs_p": null,
"transcript": "ENST00000454993.6",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2370,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000454993.6"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.2599T>A",
"hgvs_p": "p.Ser867Thr",
"transcript": "ENST00000933564.1",
"protein_id": "ENSP00000603623.1",
"transcript_support_level": null,
"aa_start": 867,
"aa_end": null,
"aa_length": 993,
"cds_start": 2599,
"cds_end": null,
"cds_length": 2982,
"cdna_start": 2696,
"cdna_end": null,
"cdna_length": 3626,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933564.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.2575T>A",
"hgvs_p": "p.Ser859Thr",
"transcript": "ENST00000933563.1",
"protein_id": "ENSP00000603622.1",
"transcript_support_level": null,
"aa_start": 859,
"aa_end": null,
"aa_length": 985,
"cds_start": 2575,
"cds_end": null,
"cds_length": 2958,
"cdna_start": 2921,
"cdna_end": null,
"cdna_length": 3849,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933563.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.2545T>A",
"hgvs_p": "p.Ser849Thr",
"transcript": "ENST00000933560.1",
"protein_id": "ENSP00000603619.1",
"transcript_support_level": null,
"aa_start": 849,
"aa_end": null,
"aa_length": 975,
"cds_start": 2545,
"cds_end": null,
"cds_length": 2928,
"cdna_start": 3595,
"cdna_end": null,
"cdna_length": 4528,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933560.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.2446T>A",
"hgvs_p": "p.Ser816Thr",
"transcript": "ENST00000933561.1",
"protein_id": "ENSP00000603620.1",
"transcript_support_level": null,
"aa_start": 816,
"aa_end": null,
"aa_length": 942,
"cds_start": 2446,
"cds_end": null,
"cds_length": 2829,
"cdna_start": 3458,
"cdna_end": null,
"cdna_length": 4396,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933561.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.1783T>A",
"hgvs_p": "p.Ser595Thr",
"transcript": "ENST00000933562.1",
"protein_id": "ENSP00000603621.1",
"transcript_support_level": null,
"aa_start": 595,
"aa_end": null,
"aa_length": 721,
"cds_start": 1783,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 2170,
"cdna_end": null,
"cdna_length": 3095,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933562.1"
},
{
"aa_ref": "S",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "c.2563T>A",
"hgvs_p": "p.Ser855Thr",
"transcript": "XM_011526862.3",
"protein_id": "XP_011525164.1",
"transcript_support_level": null,
"aa_start": 855,
"aa_end": null,
"aa_length": 981,
"cds_start": 2563,
"cds_end": null,
"cds_length": 2946,
"cdna_start": 3567,
"cdna_end": null,
"cdna_length": 4497,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526862.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"hgvs_c": "n.378T>A",
"hgvs_p": null,
"transcript": "ENST00000602210.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 389,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000602210.1"
}
],
"gene_symbol": "GRIK5",
"gene_hgnc_id": 4583,
"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": 0.1476762890815735,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.026,
"revel_prediction": "Benign",
"alphamissense_score": 0.1199,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.058,
"phylop100way_prediction": "Benign",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002088.5",
"gene_symbol": "GRIK5",
"hgnc_id": 4583,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2560T>A",
"hgvs_p": "p.Ser854Thr"
}
],
"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
}