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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: 1-1336171-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1336171&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 1336171,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001330311.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.2059C>T",
"hgvs_p": "p.Pro687Ser",
"transcript": "NM_001330311.2",
"protein_id": "NP_001317240.1",
"transcript_support_level": null,
"aa_start": 687,
"aa_end": null,
"aa_length": 695,
"cds_start": 2059,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 2412,
"cdna_end": null,
"cdna_length": 3305,
"mane_select": "ENST00000378888.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330311.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.2059C>T",
"hgvs_p": "p.Pro687Ser",
"transcript": "ENST00000378888.10",
"protein_id": "ENSP00000368166.5",
"transcript_support_level": 5,
"aa_start": 687,
"aa_end": null,
"aa_length": 695,
"cds_start": 2059,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 2412,
"cdna_end": null,
"cdna_length": 3305,
"mane_select": "NM_001330311.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378888.10"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.1984C>T",
"hgvs_p": "p.Pro662Ser",
"transcript": "ENST00000378891.9",
"protein_id": "ENSP00000368169.5",
"transcript_support_level": 1,
"aa_start": 662,
"aa_end": null,
"aa_length": 670,
"cds_start": 1984,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 2031,
"cdna_end": null,
"cdna_length": 2926,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000378891.9"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.2224C>T",
"hgvs_p": "p.Pro742Ser",
"transcript": "ENST00000874577.1",
"protein_id": "ENSP00000544636.1",
"transcript_support_level": null,
"aa_start": 742,
"aa_end": null,
"aa_length": 750,
"cds_start": 2224,
"cds_end": null,
"cds_length": 2253,
"cdna_start": 2331,
"cdna_end": null,
"cdna_length": 3222,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874577.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.2149C>T",
"hgvs_p": "p.Pro717Ser",
"transcript": "ENST00000954312.1",
"protein_id": "ENSP00000624371.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 725,
"cds_start": 2149,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 3029,
"cdna_end": null,
"cdna_length": 3924,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954312.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.1999C>T",
"hgvs_p": "p.Pro667Ser",
"transcript": "ENST00000954313.1",
"protein_id": "ENSP00000624372.1",
"transcript_support_level": null,
"aa_start": 667,
"aa_end": null,
"aa_length": 675,
"cds_start": 1999,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 2390,
"cdna_end": null,
"cdna_length": 3282,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954313.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.1987C>T",
"hgvs_p": "p.Pro663Ser",
"transcript": "ENST00000954314.1",
"protein_id": "ENSP00000624373.1",
"transcript_support_level": null,
"aa_start": 663,
"aa_end": null,
"aa_length": 671,
"cds_start": 1987,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 2337,
"cdna_end": null,
"cdna_length": 3229,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954314.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.1984C>T",
"hgvs_p": "p.Pro662Ser",
"transcript": "NM_004421.3",
"protein_id": "NP_004412.2",
"transcript_support_level": null,
"aa_start": 662,
"aa_end": null,
"aa_length": 670,
"cds_start": 1984,
"cds_end": null,
"cds_length": 2013,
"cdna_start": 2337,
"cdna_end": null,
"cdna_length": 3230,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004421.3"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.1978C>T",
"hgvs_p": "p.Pro660Ser",
"transcript": "ENST00000911402.1",
"protein_id": "ENSP00000581462.1",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 668,
"cds_start": 1978,
"cds_end": null,
"cds_length": 2007,
"cdna_start": 2202,
"cdna_end": null,
"cdna_length": 3094,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911402.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"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": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.1906C>T",
"hgvs_p": "p.Pro636Ser",
"transcript": "ENST00000954315.1",
"protein_id": "ENSP00000624374.1",
"transcript_support_level": null,
"aa_start": 636,
"aa_end": null,
"aa_length": 644,
"cds_start": 1906,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 2193,
"cdna_end": null,
"cdna_length": 3026,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000954315.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.1135C>T",
"hgvs_p": "p.Pro379Ser",
"transcript": "XM_047448090.1",
"protein_id": "XP_047304046.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 387,
"cds_start": 1135,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1216,
"cdna_end": null,
"cdna_length": 2109,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448090.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.*372C>T",
"hgvs_p": null,
"transcript": "XM_005244732.5",
"protein_id": "XP_005244789.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 574,
"cds_start": null,
"cds_end": null,
"cds_length": 1725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3343,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005244732.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.*372C>T",
"hgvs_p": null,
"transcript": "XM_005244733.5",
"protein_id": "XP_005244790.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 549,
"cds_start": null,
"cds_end": null,
"cds_length": 1650,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3268,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005244733.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"hgvs_c": "c.*372C>T",
"hgvs_p": null,
"transcript": "ENST00000632445.1",
"protein_id": "ENSP00000488888.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 217,
"cds_start": null,
"cds_end": null,
"cds_length": 654,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 785,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000632445.1"
}
],
"gene_symbol": "DVL1",
"gene_hgnc_id": 3084,
"dbsnp": "rs765583811",
"frequency_reference_population": 0.000006350077,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.0000035148,
"gnomad_genomes_af": 0.0000328455,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7347243428230286,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.47,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8175,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.345,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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_001330311.2",
"gene_symbol": "DVL1",
"hgnc_id": 3084,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2059C>T",
"hgvs_p": "p.Pro687Ser"
}
],
"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
}