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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: 3-33836155-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=33836155&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 33836155,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001162429.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.946G>A",
"hgvs_p": "p.Asp316Asn",
"transcript": "NM_013374.6",
"protein_id": "NP_037506.2",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 868,
"cds_start": 946,
"cds_end": null,
"cds_length": 2607,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000307296.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013374.6"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.946G>A",
"hgvs_p": "p.Asp316Asn",
"transcript": "ENST00000307296.8",
"protein_id": "ENSP00000307387.3",
"transcript_support_level": 1,
"aa_start": 316,
"aa_end": null,
"aa_length": 868,
"cds_start": 946,
"cds_end": null,
"cds_length": 2607,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_013374.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307296.8"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.961G>A",
"hgvs_p": "p.Asp321Asn",
"transcript": "ENST00000457054.6",
"protein_id": "ENSP00000411825.2",
"transcript_support_level": 1,
"aa_start": 321,
"aa_end": null,
"aa_length": 873,
"cds_start": 961,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457054.6"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.1066G>A",
"hgvs_p": "p.Asp356Asn",
"transcript": "ENST00000965906.1",
"protein_id": "ENSP00000635965.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 908,
"cds_start": 1066,
"cds_end": null,
"cds_length": 2727,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965906.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Asp351Asn",
"transcript": "ENST00000965908.1",
"protein_id": "ENSP00000635967.1",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 903,
"cds_start": 1051,
"cds_end": null,
"cds_length": 2712,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965908.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.961G>A",
"hgvs_p": "p.Asp321Asn",
"transcript": "NM_001162429.3",
"protein_id": "NP_001155901.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 873,
"cds_start": 961,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001162429.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.943G>A",
"hgvs_p": "p.Asp315Asn",
"transcript": "ENST00000866273.1",
"protein_id": "ENSP00000536332.1",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 867,
"cds_start": 943,
"cds_end": null,
"cds_length": 2604,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866273.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.946G>A",
"hgvs_p": "p.Asp316Asn",
"transcript": "ENST00000965903.1",
"protein_id": "ENSP00000635962.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 864,
"cds_start": 946,
"cds_end": null,
"cds_length": 2595,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965903.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.928G>A",
"hgvs_p": "p.Asp310Asn",
"transcript": "ENST00000965907.1",
"protein_id": "ENSP00000635966.1",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 862,
"cds_start": 928,
"cds_end": null,
"cds_length": 2589,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965907.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.919G>A",
"hgvs_p": "p.Asp307Asn",
"transcript": "ENST00000965905.1",
"protein_id": "ENSP00000635964.1",
"transcript_support_level": null,
"aa_start": 307,
"aa_end": null,
"aa_length": 859,
"cds_start": 919,
"cds_end": null,
"cds_length": 2580,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965905.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.946G>A",
"hgvs_p": "p.Asp316Asn",
"transcript": "ENST00000866274.1",
"protein_id": "ENSP00000536333.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 832,
"cds_start": 946,
"cds_end": null,
"cds_length": 2499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866274.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.829G>A",
"hgvs_p": "p.Asp277Asn",
"transcript": "ENST00000866275.1",
"protein_id": "ENSP00000536334.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 829,
"cds_start": 829,
"cds_end": null,
"cds_length": 2490,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866275.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.946G>A",
"hgvs_p": "p.Asp316Asn",
"transcript": "ENST00000965904.1",
"protein_id": "ENSP00000635963.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 785,
"cds_start": 946,
"cds_end": null,
"cds_length": 2358,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965904.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.391G>A",
"hgvs_p": "p.Asp131Asn",
"transcript": "XM_011533252.2",
"protein_id": "XP_011531554.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 683,
"cds_start": 391,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533252.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "c.391G>A",
"hgvs_p": "p.Asp131Asn",
"transcript": "XM_047447042.1",
"protein_id": "XP_047302998.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 683,
"cds_start": 391,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447042.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "n.*153G>A",
"hgvs_p": null,
"transcript": "ENST00000412887.5",
"protein_id": "ENSP00000415150.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000412887.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "n.609G>A",
"hgvs_p": null,
"transcript": "ENST00000482561.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000482561.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "n.601G>A",
"hgvs_p": null,
"transcript": "ENST00000487821.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000487821.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "n.*176G>A",
"hgvs_p": null,
"transcript": "ENST00000648706.1",
"protein_id": "ENSP00000497537.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000648706.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "n.*153G>A",
"hgvs_p": null,
"transcript": "ENST00000412887.5",
"protein_id": "ENSP00000415150.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000412887.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"hgvs_c": "n.*176G>A",
"hgvs_p": null,
"transcript": "ENST00000648706.1",
"protein_id": "ENSP00000497537.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000648706.1"
}
],
"gene_symbol": "PDCD6IP",
"gene_hgnc_id": 8766,
"dbsnp": "rs772115635",
"frequency_reference_population": 0.000010552609,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000109678,
"gnomad_genomes_af": 0.00000657212,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9236307144165039,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.309,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7223,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.986,
"phylop100way_prediction": "Pathogenic",
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001162429.3",
"gene_symbol": "PDCD6IP",
"hgnc_id": 8766,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.961G>A",
"hgvs_p": "p.Asp321Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}