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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: 9-94603557-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=94603557&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 94603557,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000375326.9",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBP1",
"gene_hgnc_id": 3606,
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Glu281Lys",
"transcript": "NM_000507.4",
"protein_id": "NP_000498.2",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 338,
"cds_start": 841,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 1049,
"cdna_end": null,
"cdna_length": 1473,
"mane_select": "ENST00000375326.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBP1",
"gene_hgnc_id": 3606,
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Glu281Lys",
"transcript": "ENST00000375326.9",
"protein_id": "ENSP00000364475.5",
"transcript_support_level": 1,
"aa_start": 281,
"aa_end": null,
"aa_length": 338,
"cds_start": 841,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 1049,
"cdna_end": null,
"cdna_length": 1473,
"mane_select": "NM_000507.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "FBP1",
"gene_hgnc_id": 3606,
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Glu281Lys",
"transcript": "NM_001127628.2",
"protein_id": "NP_001121100.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 338,
"cds_start": 841,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 1085,
"cdna_end": null,
"cdna_length": 1509,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "FBP1",
"gene_hgnc_id": 3606,
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Glu281Lys",
"transcript": "ENST00000415431.5",
"protein_id": "ENSP00000408025.1",
"transcript_support_level": 2,
"aa_start": 281,
"aa_end": null,
"aa_length": 338,
"cds_start": 841,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 1071,
"cdna_end": null,
"cdna_length": 1487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"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": "FBP1",
"gene_hgnc_id": 3606,
"hgvs_c": "c.646G>A",
"hgvs_p": "p.Glu216Lys",
"transcript": "ENST00000648117.1",
"protein_id": "ENSP00000498145.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 273,
"cds_start": 646,
"cds_end": null,
"cds_length": 822,
"cdna_start": 649,
"cdna_end": null,
"cdna_length": 1073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBP1",
"gene_hgnc_id": 3606,
"hgvs_c": "c.595G>A",
"hgvs_p": "p.Glu199Lys",
"transcript": "XM_006717005.5",
"protein_id": "XP_006717068.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 256,
"cds_start": 595,
"cds_end": null,
"cds_length": 771,
"cdna_start": 891,
"cdna_end": null,
"cdna_length": 1315,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCAT7",
"gene_hgnc_id": 48824,
"hgvs_c": "n.1909C>T",
"hgvs_p": null,
"transcript": "ENST00000647389.1",
"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": 2342,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBP1",
"gene_hgnc_id": 3606,
"hgvs_c": "n.*278G>A",
"hgvs_p": null,
"transcript": "ENST00000682520.1",
"protein_id": "ENSP00000507547.1",
"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": 1424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"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": "FBP1",
"gene_hgnc_id": 3606,
"hgvs_c": "n.*278G>A",
"hgvs_p": null,
"transcript": "ENST00000682520.1",
"protein_id": "ENSP00000507547.1",
"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": 1424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FBP1",
"gene_hgnc_id": 3606,
"dbsnp": "rs566453434",
"frequency_reference_population": 0.00004150812,
"hom_count_reference_population": 0,
"allele_count_reference_population": 67,
"gnomad_exomes_af": 0.0000444641,
"gnomad_genomes_af": 0.0000131328,
"gnomad_exomes_ac": 65,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9610589742660522,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.823,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9932,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.726,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000375326.9",
"gene_symbol": "FBP1",
"hgnc_id": 3606,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.841G>A",
"hgvs_p": "p.Glu281Lys"
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000647389.1",
"gene_symbol": "PCAT7",
"hgnc_id": 48824,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1909C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Fructose-biphosphatase deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:9 LP:3",
"phenotype_combined": "not provided|Fructose-biphosphatase deficiency",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}