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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: 5-177332235-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=177332235&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 177332235,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006816.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.922G>A",
"hgvs_p": "p.Asp308Asn",
"transcript": "NM_006816.3",
"protein_id": "NP_006807.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 356,
"cds_start": 922,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000303127.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006816.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.922G>A",
"hgvs_p": "p.Asp308Asn",
"transcript": "ENST00000303127.12",
"protein_id": "ENSP00000303366.7",
"transcript_support_level": 1,
"aa_start": 308,
"aa_end": null,
"aa_length": 356,
"cds_start": 922,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006816.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000303127.12"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Asp350Asn",
"transcript": "ENST00000883396.1",
"protein_id": "ENSP00000553455.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 398,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883396.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.952G>A",
"hgvs_p": "p.Asp318Asn",
"transcript": "ENST00000883394.1",
"protein_id": "ENSP00000553453.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 366,
"cds_start": 952,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883394.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.943G>A",
"hgvs_p": "p.Asp315Asn",
"transcript": "ENST00000883395.1",
"protein_id": "ENSP00000553454.1",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 363,
"cds_start": 943,
"cds_end": null,
"cds_length": 1092,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883395.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.895G>A",
"hgvs_p": "p.Asp299Asn",
"transcript": "ENST00000883393.1",
"protein_id": "ENSP00000553452.1",
"transcript_support_level": null,
"aa_start": 299,
"aa_end": null,
"aa_length": 347,
"cds_start": 895,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883393.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.578G>A",
"hgvs_p": "p.Arg193Gln",
"transcript": "ENST00000514458.5",
"protein_id": "ENSP00000424132.1",
"transcript_support_level": 5,
"aa_start": 193,
"aa_end": null,
"aa_length": 202,
"cds_start": 578,
"cds_end": null,
"cds_length": 611,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514458.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.945G>A",
"hgvs_p": "p.Thr315Thr",
"transcript": "ENST00000515209.5",
"protein_id": "ENSP00000423998.1",
"transcript_support_level": 3,
"aa_start": 315,
"aa_end": null,
"aa_length": 325,
"cds_start": 945,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515209.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "c.*2005G>A",
"hgvs_p": null,
"transcript": "ENST00000694905.1",
"protein_id": "ENSP00000511580.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": null,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000694905.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "n.3683G>A",
"hgvs_p": null,
"transcript": "ENST00000502721.6",
"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": "ENST00000502721.6"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "n.281G>A",
"hgvs_p": null,
"transcript": "ENST00000504071.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000504071.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "n.2524G>A",
"hgvs_p": null,
"transcript": "ENST00000694904.1",
"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": "retained_intron",
"feature": "ENST00000694904.1"
},
{
"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": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"hgvs_c": "n.1103+2049G>A",
"hgvs_p": null,
"transcript": "ENST00000694903.1",
"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": "ENST00000694903.1"
}
],
"gene_symbol": "LMAN2",
"gene_hgnc_id": 16986,
"dbsnp": "rs776115883",
"frequency_reference_population": 0.0000136441895,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000143815,
"gnomad_genomes_af": 0.00000657056,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4179608225822449,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.279,
"revel_prediction": "Benign",
"alphamissense_score": 0.6785,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.905,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006816.3",
"gene_symbol": "LMAN2",
"hgnc_id": 16986,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.922G>A",
"hgvs_p": "p.Asp308Asn"
}
],
"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
}