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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: 2-29193749-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=29193749&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 29193749,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000389048.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.4338C>T",
"hgvs_p": "p.Thr1446Thr",
"transcript": "NM_004304.5",
"protein_id": "NP_004295.2",
"transcript_support_level": null,
"aa_start": 1446,
"aa_end": null,
"aa_length": 1620,
"cds_start": 4338,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 5265,
"cdna_end": null,
"cdna_length": 6240,
"mane_select": "ENST00000389048.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.4338C>T",
"hgvs_p": "p.Thr1446Thr",
"transcript": "ENST00000389048.8",
"protein_id": "ENSP00000373700.3",
"transcript_support_level": 1,
"aa_start": 1446,
"aa_end": null,
"aa_length": 1620,
"cds_start": 4338,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 5265,
"cdna_end": null,
"cdna_length": 6240,
"mane_select": "NM_004304.5",
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "n.1215C>T",
"hgvs_p": null,
"transcript": "ENST00000638605.1",
"protein_id": null,
"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": 1757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.3207C>T",
"hgvs_p": "p.Thr1069Thr",
"transcript": "ENST00000618119.4",
"protein_id": "ENSP00000482733.1",
"transcript_support_level": 5,
"aa_start": 1069,
"aa_end": null,
"aa_length": 1243,
"cds_start": 3207,
"cds_end": null,
"cds_length": 3732,
"cdna_start": 3674,
"cdna_end": null,
"cdna_length": 4646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.1134C>T",
"hgvs_p": "p.Thr378Thr",
"transcript": "NM_001353765.2",
"protein_id": "NP_001340694.1",
"transcript_support_level": null,
"aa_start": 378,
"aa_end": null,
"aa_length": 552,
"cds_start": 1134,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 1461,
"cdna_end": null,
"cdna_length": 2436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "c.1134C>T",
"hgvs_p": "p.Thr378Thr",
"transcript": "ENST00000642122.1",
"protein_id": "ENSP00000493203.1",
"transcript_support_level": null,
"aa_start": 378,
"aa_end": null,
"aa_length": 552,
"cds_start": 1134,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 1538,
"cdna_end": null,
"cdna_length": 2513,
"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": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "n.*1177C>T",
"hgvs_p": null,
"transcript": "ENST00000431873.6",
"protein_id": "ENSP00000414027.3",
"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": 2520,
"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": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"hgvs_c": "n.*1177C>T",
"hgvs_p": null,
"transcript": "ENST00000431873.6",
"protein_id": "ENSP00000414027.3",
"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": 2520,
"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": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "CLIP4",
"gene_hgnc_id": 26108,
"hgvs_c": "c.1923-3179G>A",
"hgvs_p": null,
"transcript": "ENST00000689605.1",
"protein_id": "ENSP00000508948.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 666,
"cds_start": -4,
"cds_end": null,
"cds_length": 2001,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4963,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALK",
"gene_hgnc_id": 427,
"dbsnp": "rs56132472",
"frequency_reference_population": 0.10918639,
"hom_count_reference_population": 10721,
"allele_count_reference_population": 174522,
"gnomad_exomes_af": 0.109731,
"gnomad_genomes_af": 0.104014,
"gnomad_exomes_ac": 158689,
"gnomad_genomes_ac": 15833,
"gnomad_exomes_homalt": 9749,
"gnomad_genomes_homalt": 972,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.217,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000389048.8",
"gene_symbol": "ALK",
"hgnc_id": 427,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4338C>T",
"hgvs_p": "p.Thr1446Thr"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000689605.1",
"gene_symbol": "CLIP4",
"hgnc_id": 26108,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1923-3179G>A",
"hgvs_p": null
}
],
"clinvar_disease": " 3, susceptibility to,Hereditary cancer-predisposing syndrome,Neuroblastoma,Squamous cell lung carcinoma,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|Neuroblastoma, susceptibility to, 3|not provided|Hereditary cancer-predisposing syndrome|Squamous cell lung carcinoma",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}