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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: 12-131932301-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=131932301&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 131932301,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000376649.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Arg144Trp",
"transcript": "NM_025215.6",
"protein_id": "NP_079491.2",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 427,
"cds_start": 430,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 877,
"cdna_end": null,
"cdna_length": 4041,
"mane_select": "ENST00000376649.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Arg144Trp",
"transcript": "ENST00000376649.8",
"protein_id": "ENSP00000365837.3",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 427,
"cds_start": 430,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 877,
"cdna_end": null,
"cdna_length": 4041,
"mane_select": "NM_025215.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000443358.6",
"protein_id": "ENSP00000392451.2",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 399,
"cds_start": 346,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 537,
"cdna_end": null,
"cdna_length": 1664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "NM_001002019.3",
"protein_id": "NP_001002019.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 399,
"cds_start": 346,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 485,
"cdna_end": null,
"cdna_length": 3649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "NM_001002020.3",
"protein_id": "NP_001002020.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 399,
"cds_start": 346,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 3625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000322060.9",
"protein_id": "ENSP00000324726.5",
"transcript_support_level": 5,
"aa_start": 116,
"aa_end": null,
"aa_length": 383,
"cds_start": 346,
"cds_end": null,
"cds_length": 1152,
"cdna_start": 400,
"cdna_end": null,
"cdna_length": 1206,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Arg91Trp",
"transcript": "ENST00000542167.2",
"protein_id": "ENSP00000438948.1",
"transcript_support_level": 5,
"aa_start": 91,
"aa_end": null,
"aa_length": 374,
"cds_start": 271,
"cds_end": null,
"cds_length": 1125,
"cdna_start": 1024,
"cdna_end": null,
"cdna_length": 2151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000537484.1",
"protein_id": "ENSP00000440179.1",
"transcript_support_level": 3,
"aa_start": 116,
"aa_end": null,
"aa_length": 199,
"cds_start": 346,
"cds_end": null,
"cds_length": 600,
"cdna_start": 388,
"cdna_end": null,
"cdna_length": 642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Arg144Trp",
"transcript": "ENST00000544213.5",
"protein_id": "ENSP00000445819.1",
"transcript_support_level": 5,
"aa_start": 144,
"aa_end": null,
"aa_length": 183,
"cds_start": 430,
"cds_end": null,
"cds_length": 553,
"cdna_start": 564,
"cdna_end": null,
"cdna_length": 687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000456665.6",
"protein_id": "ENSP00000409705.2",
"transcript_support_level": 5,
"aa_start": 116,
"aa_end": null,
"aa_length": 155,
"cds_start": 346,
"cds_end": null,
"cds_length": 469,
"cdna_start": 454,
"cdna_end": null,
"cdna_length": 577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000538037.5",
"protein_id": "ENSP00000440326.2",
"transcript_support_level": 5,
"aa_start": 116,
"aa_end": null,
"aa_length": 152,
"cds_start": 346,
"cds_end": null,
"cds_length": 460,
"cdna_start": 517,
"cdna_end": null,
"cdna_length": 631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000535067.5",
"protein_id": "ENSP00000443969.1",
"transcript_support_level": 3,
"aa_start": 116,
"aa_end": null,
"aa_length": 134,
"cds_start": 346,
"cds_end": null,
"cds_length": 405,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "PUS1",
"gene_hgnc_id": 15508,
"hgvs_c": "n.457C>T",
"hgvs_p": null,
"transcript": "ENST00000544662.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PUS1",
"gene_hgnc_id": 15508,
"dbsnp": "rs104894371",
"frequency_reference_population": 0.000021073824,
"hom_count_reference_population": 0,
"allele_count_reference_population": 34,
"gnomad_exomes_af": 0.0000205316,
"gnomad_genomes_af": 0.0000262788,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9409441947937012,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.744,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8897,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.822,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000376649.8",
"gene_symbol": "PUS1",
"hgnc_id": 15508,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.430C>T",
"hgvs_p": "p.Arg144Trp"
}
],
"clinvar_disease": " and sideroblastic anemia 1, lactic acidosis,Myopathy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:1",
"phenotype_combined": "Myopathy, lactic acidosis, and sideroblastic anemia 1|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}