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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: 18-53499475-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=53499475&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 53499475,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005215.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"hgvs_c": "c.4076C>T",
"hgvs_p": "p.Pro1359Leu",
"transcript": "NM_005215.4",
"protein_id": "NP_005206.2",
"transcript_support_level": null,
"aa_start": 1359,
"aa_end": null,
"aa_length": 1447,
"cds_start": 4076,
"cds_end": null,
"cds_length": 4344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000442544.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005215.4"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"hgvs_c": "c.4076C>T",
"hgvs_p": "p.Pro1359Leu",
"transcript": "ENST00000442544.7",
"protein_id": "ENSP00000389140.2",
"transcript_support_level": 1,
"aa_start": 1359,
"aa_end": null,
"aa_length": 1447,
"cds_start": 4076,
"cds_end": null,
"cds_length": 4344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005215.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442544.7"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"hgvs_c": "c.2975C>T",
"hgvs_p": "p.Pro992Leu",
"transcript": "ENST00000581580.5",
"protein_id": "ENSP00000464582.1",
"transcript_support_level": 1,
"aa_start": 992,
"aa_end": null,
"aa_length": 1076,
"cds_start": 2975,
"cds_end": null,
"cds_length": 3231,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000581580.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"hgvs_c": "c.4070C>T",
"hgvs_p": "p.Pro1357Leu",
"transcript": "XM_017025568.2",
"protein_id": "XP_016881057.1",
"transcript_support_level": null,
"aa_start": 1357,
"aa_end": null,
"aa_length": 1445,
"cds_start": 4070,
"cds_end": null,
"cds_length": 4338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025568.2"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"hgvs_c": "c.4016C>T",
"hgvs_p": "p.Pro1339Leu",
"transcript": "XM_017025569.2",
"protein_id": "XP_016881058.1",
"transcript_support_level": null,
"aa_start": 1339,
"aa_end": null,
"aa_length": 1427,
"cds_start": 4016,
"cds_end": null,
"cds_length": 4284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025569.2"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"hgvs_c": "c.4010C>T",
"hgvs_p": "p.Pro1337Leu",
"transcript": "XM_047437311.1",
"protein_id": "XP_047293267.1",
"transcript_support_level": null,
"aa_start": 1337,
"aa_end": null,
"aa_length": 1425,
"cds_start": 4010,
"cds_end": null,
"cds_length": 4278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437311.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"hgvs_c": "c.3041C>T",
"hgvs_p": "p.Pro1014Leu",
"transcript": "XM_011525844.3",
"protein_id": "XP_011524146.1",
"transcript_support_level": null,
"aa_start": 1014,
"aa_end": null,
"aa_length": 1102,
"cds_start": 3041,
"cds_end": null,
"cds_length": 3309,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011525844.3"
},
{
"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": "LOC124904304",
"gene_hgnc_id": null,
"hgvs_c": "c.330-3544G>A",
"hgvs_p": null,
"transcript": "XM_047437985.1",
"protein_id": "XP_047293941.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 137,
"cds_start": null,
"cds_end": null,
"cds_length": 414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437985.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124904304",
"gene_hgnc_id": null,
"hgvs_c": "c.329+5748G>A",
"hgvs_p": null,
"transcript": "XM_047437986.1",
"protein_id": "XP_047293942.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 129,
"cds_start": null,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437986.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124904304",
"gene_hgnc_id": null,
"hgvs_c": "c.329+5748G>A",
"hgvs_p": null,
"transcript": "XM_047437987.1",
"protein_id": "XP_047293943.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 126,
"cds_start": null,
"cds_end": null,
"cds_length": 381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437987.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"hgvs_c": "n.161C>T",
"hgvs_p": null,
"transcript": "ENST00000579702.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000579702.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LINC01917",
"gene_hgnc_id": 52736,
"hgvs_c": "n.218+5748G>A",
"hgvs_p": null,
"transcript": "ENST00000582064.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000582064.1"
},
{
"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": 5,
"intron_rank_end": null,
"gene_symbol": "LINC01917",
"gene_hgnc_id": 52736,
"hgvs_c": "n.458+5748G>A",
"hgvs_p": null,
"transcript": "ENST00000650275.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000650275.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LINC01917",
"gene_hgnc_id": 52736,
"hgvs_c": "n.713+5748G>A",
"hgvs_p": null,
"transcript": "ENST00000671412.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000671412.1"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LINC01917",
"gene_hgnc_id": 52736,
"hgvs_c": "n.240+5748G>A",
"hgvs_p": null,
"transcript": "ENST00000769529.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000769529.1"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LINC01917",
"gene_hgnc_id": 52736,
"hgvs_c": "n.817+5748G>A",
"hgvs_p": null,
"transcript": "ENST00000769530.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000769530.1"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LINC01917",
"gene_hgnc_id": 52736,
"hgvs_c": "n.346+5748G>A",
"hgvs_p": null,
"transcript": "ENST00000769531.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000769531.1"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "LOC124904304",
"gene_hgnc_id": null,
"hgvs_c": "n.164+5748G>A",
"hgvs_p": null,
"transcript": "XR_007066375.1",
"protein_id": null,
"transcript_support_level": null,
"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": "XR_007066375.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124904304",
"gene_hgnc_id": null,
"hgvs_c": "n.184+5748G>A",
"hgvs_p": null,
"transcript": "XR_007066376.1",
"protein_id": null,
"transcript_support_level": null,
"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": "XR_007066376.1"
}
],
"gene_symbol": "DCC",
"gene_hgnc_id": 2701,
"dbsnp": "rs750334840",
"frequency_reference_population": 0.000028501467,
"hom_count_reference_population": 0,
"allele_count_reference_population": 46,
"gnomad_exomes_af": 0.0000280473,
"gnomad_genomes_af": 0.0000328658,
"gnomad_exomes_ac": 41,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7490524053573608,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.355,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2967,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.85,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005215.4",
"gene_symbol": "DCC",
"hgnc_id": 2701,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.4076C>T",
"hgvs_p": "p.Pro1359Leu"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000582064.1",
"gene_symbol": "LINC01917",
"hgnc_id": 52736,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.218+5748G>A",
"hgvs_p": null
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007066375.1",
"gene_symbol": "LOC124904304",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.164+5748G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}