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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: 1-162770537-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=162770537&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 162770537,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000367921.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "NM_006182.4",
"protein_id": "NP_006173.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10086,
"mane_select": "ENST00000367921.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "ENST00000367921.8",
"protein_id": "ENSP00000356898.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10086,
"mane_select": "NM_006182.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "ENST00000367922.7",
"protein_id": "ENSP00000356899.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1529T>C",
"hgvs_p": "p.Val510Ala",
"transcript": "XM_011509588.4",
"protein_id": "XP_011507890.1",
"transcript_support_level": null,
"aa_start": 510,
"aa_end": null,
"aa_length": 559,
"cds_start": 1529,
"cds_end": null,
"cds_length": 1680,
"cdna_start": 1888,
"cdna_end": null,
"cdna_length": 2404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "n.359T>C",
"hgvs_p": null,
"transcript": "ENST00000458105.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "NM_001014796.3",
"protein_id": "NP_001014796.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "NM_001354982.2",
"protein_id": "NP_001341911.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "NM_001354983.2",
"protein_id": "NP_001341912.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10503,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "ENST00000446985.6",
"protein_id": "ENSP00000400309.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2998,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "n.281+25T>C",
"hgvs_p": null,
"transcript": "ENST00000433757.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "n.1890+25T>C",
"hgvs_p": null,
"transcript": "ENST00000672207.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "XM_011509587.3",
"protein_id": "XP_011507889.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null,
"transcript": "XM_047421554.1",
"protein_id": "XP_047277510.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 855,
"cds_start": -4,
"cds_end": null,
"cds_length": 2568,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"hgvs_c": "c.1399+25T>C",
"hgvs_p": null,
"transcript": "XM_047421565.1",
"protein_id": "XP_047277521.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 820,
"cds_start": -4,
"cds_end": null,
"cds_length": 2463,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DDR2",
"gene_hgnc_id": 2731,
"dbsnp": "rs1780003",
"frequency_reference_population": 0.99145246,
"hom_count_reference_population": 793088,
"allele_count_reference_population": 1598035,
"gnomad_exomes_af": 0.995227,
"gnomad_genomes_af": 0.95521,
"gnomad_exomes_ac": 1452822,
"gnomad_genomes_ac": 145213,
"gnomad_exomes_homalt": 723374,
"gnomad_genomes_homalt": 69714,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000010810421144924476,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.23999999463558197,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.006,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.387,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.24,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000367921.8",
"gene_symbol": "DDR2",
"hgnc_id": 2731,
"effects": [
"intron_variant"
],
"inheritance_mode": "Unknown,AR,AD",
"hgvs_c": "c.1504+25T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome,Squamous cell lung carcinoma,Warburg-cinotti syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Squamous cell lung carcinoma|not provided|Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome|Warburg-cinotti syndrome",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}