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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: 2-168901489-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=168901489&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 168901489,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_021176.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "c.158T>C",
"hgvs_p": "p.Val53Ala",
"transcript": "NM_021176.3",
"protein_id": "NP_066999.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 355,
"cds_start": 158,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000375363.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021176.3"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "c.158T>C",
"hgvs_p": "p.Val53Ala",
"transcript": "ENST00000375363.8",
"protein_id": "ENSP00000364512.3",
"transcript_support_level": 1,
"aa_start": 53,
"aa_end": null,
"aa_length": 355,
"cds_start": 158,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_021176.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375363.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "n.158T>C",
"hgvs_p": null,
"transcript": "ENST00000282075.5",
"protein_id": "ENSP00000282075.4",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000282075.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "c.-81T>C",
"hgvs_p": null,
"transcript": "XM_011511565.4",
"protein_id": "XP_011509867.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 239,
"cds_start": null,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511565.4"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "c.158T>C",
"hgvs_p": "p.Val53Ala",
"transcript": "NM_001081686.2",
"protein_id": "NP_001075155.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 154,
"cds_start": 158,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001081686.2"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "c.158T>C",
"hgvs_p": "p.Val53Ala",
"transcript": "ENST00000429379.2",
"protein_id": "ENSP00000396939.2",
"transcript_support_level": 2,
"aa_start": 53,
"aa_end": null,
"aa_length": 154,
"cds_start": 158,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000429379.2"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "c.158T>C",
"hgvs_p": "p.Val53Ala",
"transcript": "ENST00000421979.1",
"protein_id": "ENSP00000392183.1",
"transcript_support_level": 3,
"aa_start": 53,
"aa_end": null,
"aa_length": 80,
"cds_start": 158,
"cds_end": null,
"cds_length": 243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421979.1"
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "c.158T>C",
"hgvs_p": "p.Val53Ala",
"transcript": "XM_011511564.4",
"protein_id": "XP_011509866.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 279,
"cds_start": 158,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511564.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"hgvs_c": "c.-81T>C",
"hgvs_p": null,
"transcript": "XM_011511565.4",
"protein_id": "XP_011509867.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 239,
"cds_start": null,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511565.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPC25",
"gene_hgnc_id": 24031,
"hgvs_c": "c.-172-10803A>G",
"hgvs_p": null,
"transcript": "ENST00000861849.1",
"protein_id": "ENSP00000531908.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": null,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861849.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPC25",
"gene_hgnc_id": 24031,
"hgvs_c": "c.-15+11707A>G",
"hgvs_p": null,
"transcript": "ENST00000861850.1",
"protein_id": "ENSP00000531909.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": null,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861850.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPC25",
"gene_hgnc_id": 24031,
"hgvs_c": "c.-172-10803A>G",
"hgvs_p": null,
"transcript": "ENST00000451987.5",
"protein_id": "ENSP00000393322.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 114,
"cds_start": null,
"cds_end": null,
"cds_length": 346,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000451987.5"
},
{
"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": "SPC25",
"gene_hgnc_id": 24031,
"hgvs_c": "n.177-10803A>G",
"hgvs_p": null,
"transcript": "ENST00000472216.2",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000472216.2"
}
],
"gene_symbol": "G6PC2",
"gene_hgnc_id": 28906,
"dbsnp": "rs868267884",
"frequency_reference_population": 0.0000020731547,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000207315,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.38427603244781494,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.379,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1406,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.845,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_021176.3",
"gene_symbol": "G6PC2",
"hgnc_id": 28906,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.158T>C",
"hgvs_p": "p.Val53Ala"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000451987.5",
"gene_symbol": "SPC25",
"hgnc_id": 24031,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-172-10803A>G",
"hgvs_p": null
}
],
"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
}