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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: 19-1466258-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1466258&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 1466258,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005883.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2957C>T",
"hgvs_p": "p.Ala986Val",
"transcript": "NM_005883.3",
"protein_id": "NP_005874.1",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 2303,
"cds_start": 2957,
"cds_end": null,
"cds_length": 6912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000590469.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005883.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2957C>T",
"hgvs_p": "p.Ala986Val",
"transcript": "ENST00000590469.6",
"protein_id": "ENSP00000467073.2",
"transcript_support_level": 1,
"aa_start": 986,
"aa_end": null,
"aa_length": 2303,
"cds_start": 2957,
"cds_end": null,
"cds_length": 6912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005883.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590469.6"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2957C>T",
"hgvs_p": "p.Ala986Val",
"transcript": "ENST00000233607.6",
"protein_id": "ENSP00000233607.2",
"transcript_support_level": 1,
"aa_start": 986,
"aa_end": null,
"aa_length": 2303,
"cds_start": 2957,
"cds_end": null,
"cds_length": 6912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000233607.6"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2957C>T",
"hgvs_p": "p.Ala986Val",
"transcript": "ENST00000535453.5",
"protein_id": "ENSP00000442954.1",
"transcript_support_level": 1,
"aa_start": 986,
"aa_end": null,
"aa_length": 2303,
"cds_start": 2957,
"cds_end": null,
"cds_length": 6912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000535453.5"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "C19orf25",
"gene_hgnc_id": 26711,
"hgvs_c": "c.131-4434G>A",
"hgvs_p": null,
"transcript": "ENST00000588427.5",
"protein_id": "ENSP00000468000.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 71,
"cds_start": null,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000588427.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2954C>T",
"hgvs_p": "p.Ala985Val",
"transcript": "NM_001351273.1",
"protein_id": "NP_001338202.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 2302,
"cds_start": 2954,
"cds_end": null,
"cds_length": 6909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001351273.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.3029C>T",
"hgvs_p": "p.Ala1010Val",
"transcript": "XM_005259475.3",
"protein_id": "XP_005259532.1",
"transcript_support_level": null,
"aa_start": 1010,
"aa_end": null,
"aa_length": 2327,
"cds_start": 3029,
"cds_end": null,
"cds_length": 6984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005259475.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.3026C>T",
"hgvs_p": "p.Ala1009Val",
"transcript": "XM_006722607.3",
"protein_id": "XP_006722670.1",
"transcript_support_level": null,
"aa_start": 1009,
"aa_end": null,
"aa_length": 2326,
"cds_start": 3026,
"cds_end": null,
"cds_length": 6981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006722607.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2957C>T",
"hgvs_p": "p.Ala986Val",
"transcript": "XM_006722608.4",
"protein_id": "XP_006722671.3",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 2303,
"cds_start": 2957,
"cds_end": null,
"cds_length": 6912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006722608.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2957C>T",
"hgvs_p": "p.Ala986Val",
"transcript": "XM_006722609.4",
"protein_id": "XP_006722672.1",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 2303,
"cds_start": 2957,
"cds_end": null,
"cds_length": 6912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006722609.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2954C>T",
"hgvs_p": "p.Ala985Val",
"transcript": "XM_006722610.4",
"protein_id": "XP_006722673.3",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 2302,
"cds_start": 2954,
"cds_end": null,
"cds_length": 6909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006722610.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2954C>T",
"hgvs_p": "p.Ala985Val",
"transcript": "XM_047438031.1",
"protein_id": "XP_047293987.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 2302,
"cds_start": 2954,
"cds_end": null,
"cds_length": 6909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438031.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"hgvs_c": "c.2954C>T",
"hgvs_p": "p.Ala985Val",
"transcript": "XM_047438032.1",
"protein_id": "XP_047293988.1",
"transcript_support_level": null,
"aa_start": 985,
"aa_end": null,
"aa_length": 2302,
"cds_start": 2954,
"cds_end": null,
"cds_length": 6909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438032.1"
}
],
"gene_symbol": "APC2",
"gene_hgnc_id": 24036,
"dbsnp": "rs758732627",
"frequency_reference_population": 0.000091495254,
"hom_count_reference_population": 0,
"allele_count_reference_population": 140,
"gnomad_exomes_af": 0.0000907178,
"gnomad_genomes_af": 0.0000985325,
"gnomad_exomes_ac": 125,
"gnomad_genomes_ac": 15,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.044886887073516846,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.132,
"revel_prediction": "Benign",
"alphamissense_score": 0.1016,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.002,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_005883.3",
"gene_symbol": "APC2",
"hgnc_id": 24036,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.2957C>T",
"hgvs_p": "p.Ala986Val"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000588427.5",
"gene_symbol": "C19orf25",
"hgnc_id": 26711,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.131-4434G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}