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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: 1-95064934-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=95064934&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 95064934,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000370205.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG14",
"gene_hgnc_id": 28287,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Asp74Asn",
"transcript": "NM_144988.4",
"protein_id": "NP_659425.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 216,
"cds_start": 220,
"cds_end": null,
"cds_length": 651,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 9375,
"mane_select": "ENST00000370205.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG14",
"gene_hgnc_id": 28287,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Asp74Asn",
"transcript": "ENST00000370205.6",
"protein_id": "ENSP00000359224.4",
"transcript_support_level": 1,
"aa_start": 74,
"aa_end": null,
"aa_length": 216,
"cds_start": 220,
"cds_end": null,
"cds_length": 651,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 9375,
"mane_select": "NM_144988.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG14",
"gene_hgnc_id": 28287,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Asp74Asn",
"transcript": "NM_001305242.2",
"protein_id": "NP_001292171.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 155,
"cds_start": 220,
"cds_end": null,
"cds_length": 468,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 9412,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG14",
"gene_hgnc_id": 28287,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Asp74Asn",
"transcript": "XM_005270582.5",
"protein_id": "XP_005270639.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 155,
"cds_start": 220,
"cds_end": null,
"cds_length": 468,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 5592,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG14",
"gene_hgnc_id": 28287,
"hgvs_c": "n.196G>A",
"hgvs_p": null,
"transcript": "ENST00000495856.1",
"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": 446,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG14",
"gene_hgnc_id": 28287,
"hgvs_c": "n.273G>A",
"hgvs_p": null,
"transcript": "XR_001737025.2",
"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": 683,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CNN3-DT",
"gene_hgnc_id": 54176,
"hgvs_c": "n.1005-2110C>T",
"hgvs_p": null,
"transcript": "ENST00000715651.1",
"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": 1505,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CNN3-DT",
"gene_hgnc_id": 54176,
"hgvs_c": "n.595-2110C>T",
"hgvs_p": null,
"transcript": "ENST00000715652.1",
"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": 1096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALG14",
"gene_hgnc_id": 28287,
"hgvs_c": "n.189+7829G>A",
"hgvs_p": null,
"transcript": "NR_131032.2",
"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": 9223,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ALG14-AS1",
"gene_hgnc_id": 41192,
"hgvs_c": "n.595-2110C>T",
"hgvs_p": null,
"transcript": "NR_132786.1",
"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": 1096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALG14",
"gene_hgnc_id": 28287,
"dbsnp": "rs769114543",
"frequency_reference_population": 0.00022866619,
"hom_count_reference_population": 0,
"allele_count_reference_population": 369,
"gnomad_exomes_af": 0.000240843,
"gnomad_genomes_af": 0.000111714,
"gnomad_exomes_ac": 352,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9864241480827332,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.697,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9547,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.718,
"phylop100way_prediction": "Uncertain_significance",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000370205.6",
"gene_symbol": "ALG14",
"hgnc_id": 28287,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Asp74Asn"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NR_132786.1",
"gene_symbol": "ALG14-AS1",
"hgnc_id": 41192,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.595-2110C>T",
"hgvs_p": null
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PP3_Strong",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000715651.1",
"gene_symbol": "CNN3-DT",
"hgnc_id": 54176,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1005-2110C>T",
"hgvs_p": null
}
],
"clinvar_disease": " and progressive cerebral atrophy, epilepsy,Congenital myasthenic syndrome 15,Congenital myopathy,Myopathy,See cases,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:1 US:1",
"phenotype_combined": "not provided|Congenital myasthenic syndrome 15|Myopathy, epilepsy, and progressive cerebral atrophy|See cases|Congenital myopathy",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}