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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: 19-41999249-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41999249&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41999249,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_002088.5",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "W",
"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.2565C>G",
"hgvs_p": "p.Cys855Trp",
"transcript": "NM_002088.5",
"protein_id": "NP_002079.3",
"transcript_support_level": null,
"aa_start": 855,
"aa_end": null,
"aa_length": 980,
"cds_start": 2565,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 3581,
"cdna_end": null,
"cdna_length": 4506,
"mane_select": "ENST00000593562.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002088.5"
},
{
"aa_ref": "C",
"aa_alt": "W",
"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.2565C>G",
"hgvs_p": "p.Cys855Trp",
"transcript": "ENST00000593562.6",
"protein_id": "ENSP00000470251.1",
"transcript_support_level": 5,
"aa_start": 855,
"aa_end": null,
"aa_length": 980,
"cds_start": 2565,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 3581,
"cdna_end": null,
"cdna_length": 4506,
"mane_select": "NM_002088.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000593562.6"
},
{
"aa_ref": "C",
"aa_alt": "W",
"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.2565C>G",
"hgvs_p": "p.Cys855Trp",
"transcript": "ENST00000262895.7",
"protein_id": "ENSP00000262895.2",
"transcript_support_level": 1,
"aa_start": 855,
"aa_end": null,
"aa_length": 980,
"cds_start": 2565,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2565,
"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.1442C>G",
"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": "C",
"aa_alt": "W",
"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.2604C>G",
"hgvs_p": "p.Cys868Trp",
"transcript": "ENST00000933564.1",
"protein_id": "ENSP00000603623.1",
"transcript_support_level": null,
"aa_start": 868,
"aa_end": null,
"aa_length": 993,
"cds_start": 2604,
"cds_end": null,
"cds_length": 2982,
"cdna_start": 2701,
"cdna_end": null,
"cdna_length": 3626,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933564.1"
},
{
"aa_ref": "C",
"aa_alt": "W",
"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.2580C>G",
"hgvs_p": "p.Cys860Trp",
"transcript": "ENST00000933563.1",
"protein_id": "ENSP00000603622.1",
"transcript_support_level": null,
"aa_start": 860,
"aa_end": null,
"aa_length": 985,
"cds_start": 2580,
"cds_end": null,
"cds_length": 2958,
"cdna_start": 2926,
"cdna_end": null,
"cdna_length": 3849,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933563.1"
},
{
"aa_ref": "C",
"aa_alt": "W",
"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.2550C>G",
"hgvs_p": "p.Cys850Trp",
"transcript": "ENST00000933560.1",
"protein_id": "ENSP00000603619.1",
"transcript_support_level": null,
"aa_start": 850,
"aa_end": null,
"aa_length": 975,
"cds_start": 2550,
"cds_end": null,
"cds_length": 2928,
"cdna_start": 3600,
"cdna_end": null,
"cdna_length": 4528,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933560.1"
},
{
"aa_ref": "C",
"aa_alt": "W",
"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.2451C>G",
"hgvs_p": "p.Cys817Trp",
"transcript": "ENST00000933561.1",
"protein_id": "ENSP00000603620.1",
"transcript_support_level": null,
"aa_start": 817,
"aa_end": null,
"aa_length": 942,
"cds_start": 2451,
"cds_end": null,
"cds_length": 2829,
"cdna_start": 3463,
"cdna_end": null,
"cdna_length": 4396,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933561.1"
},
{
"aa_ref": "C",
"aa_alt": "W",
"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.1788C>G",
"hgvs_p": "p.Cys596Trp",
"transcript": "ENST00000933562.1",
"protein_id": "ENSP00000603621.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 721,
"cds_start": 1788,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 2175,
"cdna_end": null,
"cdna_length": 3095,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933562.1"
},
{
"aa_ref": "C",
"aa_alt": "W",
"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.2568C>G",
"hgvs_p": "p.Cys856Trp",
"transcript": "XM_011526862.3",
"protein_id": "XP_011525164.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 981,
"cds_start": 2568,
"cds_end": null,
"cds_length": 2946,
"cdna_start": 3572,
"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.383C>G",
"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": "rs1193861383",
"frequency_reference_population": 0.000011149413,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000109277,
"gnomad_genomes_af": 0.0000131508,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.48945480585098267,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.169,
"revel_prediction": "Benign",
"alphamissense_score": 0.8652,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.678,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002088.5",
"gene_symbol": "GRIK5",
"hgnc_id": 4583,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2565C>G",
"hgvs_p": "p.Cys855Trp"
}
],
"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
}