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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: 16-21159374-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=21159374&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 21159374,
"ref": "C",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000233047.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH3",
"gene_hgnc_id": 2949,
"hgvs_c": "c.68G>T",
"hgvs_p": "p.Arg23Leu",
"transcript": "ENST00000261383.3",
"protein_id": "ENSP00000261383.3",
"transcript_support_level": 1,
"aa_start": 23,
"aa_end": null,
"aa_length": 4116,
"cds_start": 68,
"cds_end": null,
"cds_length": 12351,
"cdna_start": 68,
"cdna_end": null,
"cdna_length": 12394,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "c.-99+628C>A",
"hgvs_p": null,
"transcript": "NM_001301771.2",
"protein_id": "NP_001288700.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 161,
"cds_start": -4,
"cds_end": null,
"cds_length": 486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1717,
"mane_select": "ENST00000233047.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "c.-99+628C>A",
"hgvs_p": null,
"transcript": "ENST00000233047.9",
"protein_id": "ENSP00000233047.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 161,
"cds_start": -4,
"cds_end": null,
"cds_length": 486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1717,
"mane_select": "NM_001301771.2",
"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": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "n.-99+628C>A",
"hgvs_p": null,
"transcript": "ENST00000573487.5",
"protein_id": "ENSP00000461828.1",
"transcript_support_level": 1,
"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": 1593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH3",
"gene_hgnc_id": 2949,
"hgvs_c": "c.68G>T",
"hgvs_p": "p.Arg23Leu",
"transcript": "ENST00000685858.1",
"protein_id": "ENSP00000508756.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 4130,
"cds_start": 68,
"cds_end": null,
"cds_length": 12393,
"cdna_start": 68,
"cdna_end": null,
"cdna_length": 12436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH3",
"gene_hgnc_id": 2949,
"hgvs_c": "c.68G>T",
"hgvs_p": "p.Arg23Leu",
"transcript": "NM_017539.2",
"protein_id": "NP_060009.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 4116,
"cds_start": 68,
"cds_end": null,
"cds_length": 12351,
"cdna_start": 68,
"cdna_end": null,
"cdna_length": 12394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH3",
"gene_hgnc_id": 2949,
"hgvs_c": "c.68G>T",
"hgvs_p": "p.Arg23Leu",
"transcript": "XM_017023432.2",
"protein_id": "XP_016878921.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 4130,
"cds_start": 68,
"cds_end": null,
"cds_length": 12393,
"cdna_start": 86,
"cdna_end": null,
"cdna_length": 12454,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "c.-99+628C>A",
"hgvs_p": null,
"transcript": "NM_001301775.2",
"protein_id": "NP_001288704.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 185,
"cds_start": -4,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1789,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "c.-99+628C>A",
"hgvs_p": null,
"transcript": "ENST00000451578.6",
"protein_id": "ENSP00000409879.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 185,
"cds_start": -4,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "c.-130+628C>A",
"hgvs_p": null,
"transcript": "NM_001301769.2",
"protein_id": "NP_001288698.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 161,
"cds_start": -4,
"cds_end": null,
"cds_length": 486,
"cdna_start": null,
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"cdna_length": 1748,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "c.-206+628C>A",
"hgvs_p": null,
"transcript": "NM_020422.6",
"protein_id": "NP_065155.3",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1824,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 5,
"intron_rank": 1,
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"gene_symbol": "LDAF1",
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"hgvs_c": "c.-206+628C>A",
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"transcript": "ENST00000261388.7",
"protein_id": "ENSP00000261388.3",
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},
{
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"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 1,
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"gene_symbol": "LDAF1",
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"hgvs_c": "c.-130+628C>A",
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"transcript": "ENST00000572599.5",
"protein_id": "ENSP00000460687.1",
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},
{
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"strand": true,
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],
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"exon_count": 4,
"intron_rank": 1,
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"gene_symbol": "LDAF1",
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"hgvs_c": "c.-206+628C>A",
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"transcript": "NM_001301773.2",
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},
{
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],
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"gene_symbol": "LDAF1",
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"hgvs_c": "c.-99+628C>A",
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"transcript": "NM_001301774.2",
"protein_id": "NP_001288703.1",
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},
{
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"strand": true,
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],
"exon_rank": null,
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"exon_count": 4,
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"gene_symbol": "LDAF1",
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"hgvs_c": "c.-99+628C>A",
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"transcript": "ENST00000572258.5",
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},
{
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],
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"gene_symbol": "LDAF1",
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"hgvs_c": "c.-130+628C>A",
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"transcript": "ENST00000577162.1",
"protein_id": "ENSP00000461826.1",
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
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],
"exon_rank": null,
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"exon_count": 4,
"intron_rank": 1,
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"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "n.73+628C>A",
"hgvs_p": null,
"transcript": "ENST00000574092.1",
"protein_id": null,
"transcript_support_level": 5,
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},
{
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"strand": true,
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],
"exon_rank": null,
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"exon_count": 7,
"intron_rank": 1,
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"gene_symbol": "LDAF1",
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"hgvs_c": "n.73+628C>A",
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"transcript": "NR_125971.2",
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},
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],
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"gene_symbol": "LDAF1",
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},
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],
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"gene_symbol": "LDAF1",
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},
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"consequences": [
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],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 1,
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"gene_symbol": "LDAF1",
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"hgvs_c": "c.-99+628C>A",
"hgvs_p": null,
"transcript": "XM_047434368.1",
"protein_id": "XP_047290324.1",
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LDAF1",
"gene_hgnc_id": 30136,
"hgvs_c": "c.-206+628C>A",
"hgvs_p": null,
"transcript": "XM_006721067.5",
"protein_id": "XP_006721130.1",
"transcript_support_level": null,
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},
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{
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}
],
"gene_symbol": "LDAF1",
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"dbsnp": null,
"frequency_reference_population": 6.8406376e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84064e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03410354256629944,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.006,
"revel_prediction": "Benign",
"alphamissense_score": 0.1128,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.011,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000233047.9",
"gene_symbol": "LDAF1",
"hgnc_id": 30136,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.-99+628C>A",
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},
{
"score": -2,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_017539.2",
"gene_symbol": "DNAH3",
"hgnc_id": 2949,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.68G>T",
"hgvs_p": "p.Arg23Leu"
}
],
"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
}