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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: 3-142512266-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=142512266&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 142512266,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000350721.9",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4846T>G",
"hgvs_p": "p.Ser1616Ala",
"transcript": "NM_001184.4",
"protein_id": "NP_001175.2",
"transcript_support_level": null,
"aa_start": 1616,
"aa_end": null,
"aa_length": 2644,
"cds_start": 4846,
"cds_end": null,
"cds_length": 7935,
"cdna_start": 4875,
"cdna_end": null,
"cdna_length": 8158,
"mane_select": "ENST00000350721.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4846T>G",
"hgvs_p": "p.Ser1616Ala",
"transcript": "ENST00000350721.9",
"protein_id": "ENSP00000343741.4",
"transcript_support_level": 1,
"aa_start": 1616,
"aa_end": null,
"aa_length": 2644,
"cds_start": 4846,
"cds_end": null,
"cds_length": 7935,
"cdna_start": 4875,
"cdna_end": null,
"cdna_length": 8158,
"mane_select": "NM_001184.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4654T>G",
"hgvs_p": "p.Ser1552Ala",
"transcript": "NM_001354579.2",
"protein_id": "NP_001341508.1",
"transcript_support_level": null,
"aa_start": 1552,
"aa_end": null,
"aa_length": 2580,
"cds_start": 4654,
"cds_end": null,
"cds_length": 7743,
"cdna_start": 4683,
"cdna_end": null,
"cdna_length": 7966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4654T>G",
"hgvs_p": "p.Ser1552Ala",
"transcript": "ENST00000661310.1",
"protein_id": "ENSP00000499589.1",
"transcript_support_level": null,
"aa_start": 1552,
"aa_end": null,
"aa_length": 2580,
"cds_start": 4654,
"cds_end": null,
"cds_length": 7743,
"cdna_start": 4673,
"cdna_end": null,
"cdna_length": 7838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4852T>G",
"hgvs_p": "p.Ser1618Ala",
"transcript": "XM_011512924.2",
"protein_id": "XP_011511226.1",
"transcript_support_level": null,
"aa_start": 1618,
"aa_end": null,
"aa_length": 2646,
"cds_start": 4852,
"cds_end": null,
"cds_length": 7941,
"cdna_start": 4881,
"cdna_end": null,
"cdna_length": 8164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4852T>G",
"hgvs_p": "p.Ser1618Ala",
"transcript": "XM_047448360.1",
"protein_id": "XP_047304316.1",
"transcript_support_level": null,
"aa_start": 1618,
"aa_end": null,
"aa_length": 2612,
"cds_start": 4852,
"cds_end": null,
"cds_length": 7839,
"cdna_start": 4881,
"cdna_end": null,
"cdna_length": 10365,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4852T>G",
"hgvs_p": "p.Ser1618Ala",
"transcript": "XM_047448361.1",
"protein_id": "XP_047304317.1",
"transcript_support_level": null,
"aa_start": 1618,
"aa_end": null,
"aa_length": 2598,
"cds_start": 4852,
"cds_end": null,
"cds_length": 7797,
"cdna_start": 4881,
"cdna_end": null,
"cdna_length": 7840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4660T>G",
"hgvs_p": "p.Ser1554Ala",
"transcript": "XM_011512925.2",
"protein_id": "XP_011511227.1",
"transcript_support_level": null,
"aa_start": 1554,
"aa_end": null,
"aa_length": 2582,
"cds_start": 4660,
"cds_end": null,
"cds_length": 7749,
"cdna_start": 4689,
"cdna_end": null,
"cdna_length": 7972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4852T>G",
"hgvs_p": "p.Ser1618Ala",
"transcript": "XM_047448362.1",
"protein_id": "XP_047304318.1",
"transcript_support_level": null,
"aa_start": 1618,
"aa_end": null,
"aa_length": 2082,
"cds_start": 4852,
"cds_end": null,
"cds_length": 6249,
"cdna_start": 4881,
"cdna_end": null,
"cdna_length": 6349,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4846T>G",
"hgvs_p": "p.Ser1616Ala",
"transcript": "XM_047448363.1",
"protein_id": "XP_047304319.1",
"transcript_support_level": null,
"aa_start": 1616,
"aa_end": null,
"aa_length": 2080,
"cds_start": 4846,
"cds_end": null,
"cds_length": 6243,
"cdna_start": 4875,
"cdna_end": null,
"cdna_length": 6349,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "c.4852T>G",
"hgvs_p": "p.Ser1618Ala",
"transcript": "XM_047448364.1",
"protein_id": "XP_047304320.1",
"transcript_support_level": null,
"aa_start": 1618,
"aa_end": null,
"aa_length": 1891,
"cds_start": 4852,
"cds_end": null,
"cds_length": 5676,
"cdna_start": 4881,
"cdna_end": null,
"cdna_length": 5807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.4875T>G",
"hgvs_p": null,
"transcript": "ENST00000653868.1",
"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": 8096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.3634T>G",
"hgvs_p": null,
"transcript": "ENST00000656590.1",
"protein_id": "ENSP00000499225.1",
"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": 7056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"hgvs_c": "n.310T>G",
"hgvs_p": null,
"transcript": "ENST00000666943.1",
"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": 4763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATR",
"gene_hgnc_id": 882,
"dbsnp": "rs201492267",
"frequency_reference_population": 0.00010194932,
"hom_count_reference_population": 0,
"allele_count_reference_population": 161,
"gnomad_exomes_af": 0.000108399,
"gnomad_genomes_af": 0.0000401838,
"gnomad_exomes_ac": 155,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01657453179359436,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.01,
"revel_prediction": "Benign",
"alphamissense_score": 0.0585,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.392,
"phylop100way_prediction": "Benign",
"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": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000350721.9",
"gene_symbol": "ATR",
"hgnc_id": 882,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.4846T>G",
"hgvs_p": "p.Ser1616Ala"
}
],
"clinvar_disease": "Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome,Seckel syndrome 1,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:6",
"phenotype_combined": "Seckel syndrome 1|not provided|Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome;Seckel syndrome 1|Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}