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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: 1-1336180-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1336180&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP3",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DVL1",
"hgnc_id": 3084,
"hgvs_c": "c.2050A>G",
"hgvs_p": "p.Met684Val",
"inheritance_mode": "AD",
"pathogenic_score": 1,
"score": -3,
"transcript": "NM_001330311.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_score": -3,
"allele_count_reference_population": 15,
"alphamissense_prediction": null,
"alphamissense_score": 0.3002,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.793099045753479,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 695,
"aa_ref": "M",
"aa_start": 684,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3305,
"cdna_start": 2403,
"cds_end": null,
"cds_length": 2088,
"cds_start": 2050,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_001330311.2",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.2050A>G",
"hgvs_p": "p.Met684Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000378888.10",
"protein_coding": true,
"protein_id": "NP_001317240.1",
"strand": false,
"transcript": "NM_001330311.2",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 695,
"aa_ref": "M",
"aa_start": 684,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3305,
"cdna_start": 2403,
"cds_end": null,
"cds_length": 2088,
"cds_start": 2050,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000378888.10",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.2050A>G",
"hgvs_p": "p.Met684Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001330311.2",
"protein_coding": true,
"protein_id": "ENSP00000368166.5",
"strand": false,
"transcript": "ENST00000378888.10",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 670,
"aa_ref": "M",
"aa_start": 659,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2926,
"cdna_start": 2022,
"cds_end": null,
"cds_length": 2013,
"cds_start": 1975,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000378891.9",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.1975A>G",
"hgvs_p": "p.Met659Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000368169.5",
"strand": false,
"transcript": "ENST00000378891.9",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 750,
"aa_ref": "M",
"aa_start": 739,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3222,
"cdna_start": 2322,
"cds_end": null,
"cds_length": 2253,
"cds_start": 2215,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000874577.1",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.2215A>G",
"hgvs_p": "p.Met739Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544636.1",
"strand": false,
"transcript": "ENST00000874577.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 725,
"aa_ref": "M",
"aa_start": 714,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3924,
"cdna_start": 3020,
"cds_end": null,
"cds_length": 2178,
"cds_start": 2140,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000954312.1",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.2140A>G",
"hgvs_p": "p.Met714Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624371.1",
"strand": false,
"transcript": "ENST00000954312.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 675,
"aa_ref": "M",
"aa_start": 664,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3282,
"cdna_start": 2381,
"cds_end": null,
"cds_length": 2028,
"cds_start": 1990,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000954313.1",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.1990A>G",
"hgvs_p": "p.Met664Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624372.1",
"strand": false,
"transcript": "ENST00000954313.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 671,
"aa_ref": "M",
"aa_start": 660,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3229,
"cdna_start": 2328,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1978,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000954314.1",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.1978A>G",
"hgvs_p": "p.Met660Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624373.1",
"strand": false,
"transcript": "ENST00000954314.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 670,
"aa_ref": "M",
"aa_start": 659,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3230,
"cdna_start": 2328,
"cds_end": null,
"cds_length": 2013,
"cds_start": 1975,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_004421.3",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.1975A>G",
"hgvs_p": "p.Met659Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_004412.2",
"strand": false,
"transcript": "NM_004421.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 668,
"aa_ref": "M",
"aa_start": 657,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3094,
"cdna_start": 2193,
"cds_end": null,
"cds_length": 2007,
"cds_start": 1969,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000911402.1",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.1969A>G",
"hgvs_p": "p.Met657Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581462.1",
"strand": false,
"transcript": "ENST00000911402.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 644,
"aa_ref": "M",
"aa_start": 633,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3026,
"cdna_start": 2184,
"cds_end": null,
"cds_length": 1935,
"cds_start": 1897,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000954315.1",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.1897A>G",
"hgvs_p": "p.Met633Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624374.1",
"strand": false,
"transcript": "ENST00000954315.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 387,
"aa_ref": "M",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2109,
"cdna_start": 1207,
"cds_end": null,
"cds_length": 1164,
"cds_start": 1126,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047448090.1",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.1126A>G",
"hgvs_p": "p.Met376Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304046.1",
"strand": false,
"transcript": "XM_047448090.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 574,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3343,
"cdna_start": null,
"cds_end": null,
"cds_length": 1725,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_005244732.5",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.*363A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005244789.1",
"strand": false,
"transcript": "XM_005244732.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 549,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3268,
"cdna_start": null,
"cds_end": null,
"cds_length": 1650,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_005244733.5",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.*363A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005244790.1",
"strand": false,
"transcript": "XM_005244733.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 217,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 785,
"cdna_start": null,
"cds_end": null,
"cds_length": 654,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000632445.1",
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"hgvs_c": "c.*363A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000488888.1",
"strand": true,
"transcript": "ENST00000632445.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs867309666",
"effect": "missense_variant",
"frequency_reference_population": 0.000009534209,
"gene_hgnc_id": 3084,
"gene_symbol": "DVL1",
"gnomad_exomes_ac": 14,
"gnomad_exomes_af": 0.00000985151,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657117,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.591,
"pos": 1336180,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.283,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001330311.2"
}
]
}