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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: 1-154992746-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=154992746&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 154992746,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_025207.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.1588C>T",
"hgvs_p": "p.Arg530Cys",
"transcript": "NM_025207.5",
"protein_id": "NP_079483.3",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 587,
"cds_start": 1588,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 1939,
"cdna_end": null,
"cdna_length": 2189,
"mane_select": "ENST00000292180.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.1588C>T",
"hgvs_p": "p.Arg530Cys",
"transcript": "ENST00000292180.8",
"protein_id": "ENSP00000292180.3",
"transcript_support_level": 1,
"aa_start": 530,
"aa_end": null,
"aa_length": 587,
"cds_start": 1588,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 1939,
"cdna_end": null,
"cdna_length": 2189,
"mane_select": "NM_025207.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.1297C>T",
"hgvs_p": "p.Arg433Cys",
"transcript": "ENST00000315144.14",
"protein_id": "ENSP00000317296.10",
"transcript_support_level": 1,
"aa_start": 433,
"aa_end": null,
"aa_length": 490,
"cds_start": 1297,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1480,
"cdna_end": null,
"cdna_length": 1730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.1297C>T",
"hgvs_p": "p.Arg433Cys",
"transcript": "ENST00000368432.5",
"protein_id": "ENSP00000357417.1",
"transcript_support_level": 1,
"aa_start": 433,
"aa_end": null,
"aa_length": 446,
"cds_start": 1297,
"cds_end": null,
"cds_length": 1341,
"cdna_start": 1474,
"cdna_end": null,
"cdna_length": 1839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.*11+73C>T",
"hgvs_p": null,
"transcript": "ENST00000295530.6",
"protein_id": "ENSP00000295530.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 170,
"cds_start": -4,
"cds_end": null,
"cds_length": 513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1211,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.1297C>T",
"hgvs_p": "p.Arg433Cys",
"transcript": "NM_201398.3",
"protein_id": "NP_958800.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 490,
"cds_start": 1297,
"cds_end": null,
"cds_length": 1473,
"cdna_start": 1495,
"cdna_end": null,
"cdna_length": 1745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.1297C>T",
"hgvs_p": "p.Arg433Cys",
"transcript": "NM_001184891.2",
"protein_id": "NP_001171820.1",
"transcript_support_level": null,
"aa_start": 433,
"aa_end": null,
"aa_length": 446,
"cds_start": 1297,
"cds_end": null,
"cds_length": 1341,
"cdna_start": 1495,
"cdna_end": null,
"cdna_length": 1860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"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": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.211C>T",
"hgvs_p": "p.Arg71Cys",
"transcript": "ENST00000368428.1",
"protein_id": "ENSP00000357413.1",
"transcript_support_level": 3,
"aa_start": 71,
"aa_end": null,
"aa_length": 128,
"cds_start": 211,
"cds_end": null,
"cds_length": 387,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 1111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.787C>T",
"hgvs_p": "p.Arg263Cys",
"transcript": "XM_047430941.1",
"protein_id": "XP_047286897.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 320,
"cds_start": 787,
"cds_end": null,
"cds_length": 963,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 1520,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "n.158C>T",
"hgvs_p": null,
"transcript": "ENST00000481758.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 408,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "n.398C>T",
"hgvs_p": null,
"transcript": "ENST00000489992.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 648,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "c.*155C>T",
"hgvs_p": null,
"transcript": "XM_047430940.1",
"protein_id": "XP_047286896.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 429,
"cds_start": -4,
"cds_end": null,
"cds_length": 1290,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"hgvs_c": "n.344+73C>T",
"hgvs_p": null,
"transcript": "ENST00000477609.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FLAD1",
"gene_hgnc_id": 24671,
"dbsnp": "rs771466122",
"frequency_reference_population": 0.000024163568,
"hom_count_reference_population": 0,
"allele_count_reference_population": 39,
"gnomad_exomes_af": 0.0000218894,
"gnomad_genomes_af": 0.0000460205,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8818994760513306,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.628,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2784,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.406,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.18,
"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": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_025207.5",
"gene_symbol": "FLAD1",
"hgnc_id": 24671,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1588C>T",
"hgvs_p": "p.Arg530Cys"
}
],
"clinvar_disease": "FLAD1-related disorder,Multiple acyl-CoA dehydrogenase deficiency,Myopathy with abnormal lipid metabolism,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": "Multiple acyl-CoA dehydrogenase deficiency|Myopathy with abnormal lipid metabolism|not provided|FLAD1-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}