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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: 3-196241987-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196241987&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 196241987,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_005017.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg",
"transcript": "NM_001312673.2",
"protein_id": "NP_001299602.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000431016.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001312673.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg",
"transcript": "ENST00000431016.6",
"protein_id": "ENSP00000394617.1",
"transcript_support_level": 1,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001312673.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000431016.6"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg",
"transcript": "ENST00000292823.6",
"protein_id": "ENSP00000292823.2",
"transcript_support_level": 1,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000292823.6"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg",
"transcript": "ENST00000419333.5",
"protein_id": "ENSP00000390968.1",
"transcript_support_level": 5,
"aa_start": 223,
"aa_end": null,
"aa_length": 380,
"cds_start": 669,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000419333.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg",
"transcript": "NM_005017.4",
"protein_id": "NP_005008.2",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005017.4"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg",
"transcript": "ENST00000875586.1",
"protein_id": "ENSP00000545645.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 367,
"cds_start": 669,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875586.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.666G>A",
"hgvs_p": "p.Arg222Arg",
"transcript": "ENST00000875587.1",
"protein_id": "ENSP00000545646.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 366,
"cds_start": 666,
"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": "ENST00000875587.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.636G>A",
"hgvs_p": "p.Arg212Arg",
"transcript": "ENST00000875583.1",
"protein_id": "ENSP00000545642.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 356,
"cds_start": 636,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875583.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.636G>A",
"hgvs_p": "p.Arg212Arg",
"transcript": "ENST00000928611.1",
"protein_id": "ENSP00000598670.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 356,
"cds_start": 636,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928611.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg",
"transcript": "ENST00000875584.1",
"protein_id": "ENSP00000545643.1",
"transcript_support_level": null,
"aa_start": 223,
"aa_end": null,
"aa_length": 304,
"cds_start": 669,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875584.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg",
"transcript": "ENST00000411591.5",
"protein_id": "ENSP00000400430.1",
"transcript_support_level": 3,
"aa_start": 223,
"aa_end": null,
"aa_length": 292,
"cds_start": 669,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000411591.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.471G>A",
"hgvs_p": "p.Arg157Arg",
"transcript": "ENST00000430755.5",
"protein_id": "ENSP00000402283.1",
"transcript_support_level": 3,
"aa_start": 157,
"aa_end": null,
"aa_length": 201,
"cds_start": 471,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000430755.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.288G>A",
"hgvs_p": "p.Arg96Arg",
"transcript": "ENST00000433733.5",
"protein_id": "ENSP00000390458.1",
"transcript_support_level": 5,
"aa_start": 96,
"aa_end": null,
"aa_length": 136,
"cds_start": 288,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000433733.5"
},
{
"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": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.487-2252G>A",
"hgvs_p": null,
"transcript": "ENST00000875585.1",
"protein_id": "ENSP00000545644.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 293,
"cds_start": null,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875585.1"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "c.486+5380G>A",
"hgvs_p": null,
"transcript": "ENST00000441879.5",
"protein_id": "ENSP00000392397.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": null,
"cds_end": null,
"cds_length": 638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441879.5"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC51A",
"gene_hgnc_id": 29955,
"hgvs_c": "c.58-507C>T",
"hgvs_p": null,
"transcript": "ENST00000415111.1",
"protein_id": "ENSP00000409560.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 23,
"cds_start": null,
"cds_end": null,
"cds_length": 72,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415111.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"hgvs_c": "n.*80G>A",
"hgvs_p": null,
"transcript": "ENST00000473978.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000473978.5"
}
],
"gene_symbol": "PCYT1A",
"gene_hgnc_id": 8754,
"dbsnp": "rs540053239",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3199999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.107,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP7",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_005017.4",
"gene_symbol": "PCYT1A",
"hgnc_id": 8754,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.669G>A",
"hgvs_p": "p.Arg223Arg"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000415111.1",
"gene_symbol": "SLC51A",
"hgnc_id": 29955,
"effects": [
"intron_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.58-507C>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}