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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: 14-23417598-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=23417598&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 23417598,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000355349.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYH7",
"gene_hgnc_id": 7577,
"hgvs_c": "c.4258C>T",
"hgvs_p": "p.Arg1420Trp",
"transcript": "NM_000257.4",
"protein_id": "NP_000248.2",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1935,
"cds_start": 4258,
"cds_end": null,
"cds_length": 5808,
"cdna_start": 4363,
"cdna_end": null,
"cdna_length": 6027,
"mane_select": "ENST00000355349.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYH7",
"gene_hgnc_id": 7577,
"hgvs_c": "c.4258C>T",
"hgvs_p": "p.Arg1420Trp",
"transcript": "ENST00000355349.4",
"protein_id": "ENSP00000347507.3",
"transcript_support_level": 1,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1935,
"cds_start": 4258,
"cds_end": null,
"cds_length": 5808,
"cdna_start": 4363,
"cdna_end": null,
"cdna_length": 6027,
"mane_select": "NM_000257.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYH7",
"gene_hgnc_id": 7577,
"hgvs_c": "c.4258C>T",
"hgvs_p": "p.Arg1420Trp",
"transcript": "ENST00000713768.1",
"protein_id": "ENSP00000519070.1",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1944,
"cds_start": 4258,
"cds_end": null,
"cds_length": 5835,
"cdna_start": 4363,
"cdna_end": null,
"cdna_length": 6103,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYH7",
"gene_hgnc_id": 7577,
"hgvs_c": "c.4258C>T",
"hgvs_p": "p.Arg1420Trp",
"transcript": "NM_001407004.1",
"protein_id": "NP_001393933.1",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1935,
"cds_start": 4258,
"cds_end": null,
"cds_length": 5808,
"cdna_start": 4307,
"cdna_end": null,
"cdna_length": 5971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYH7",
"gene_hgnc_id": 7577,
"hgvs_c": "c.4258C>T",
"hgvs_p": "p.Arg1420Trp",
"transcript": "ENST00000713769.1",
"protein_id": "ENSP00000519071.1",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1935,
"cds_start": 4258,
"cds_end": null,
"cds_length": 5808,
"cdna_start": 4307,
"cdna_end": null,
"cdna_length": 5971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MHRT",
"gene_hgnc_id": 51291,
"hgvs_c": "n.*3G>A",
"hgvs_p": null,
"transcript": "NR_126491.1",
"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": 876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MYH7",
"gene_hgnc_id": 7577,
"dbsnp": "rs145213771",
"frequency_reference_population": 0.000013022222,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000130101,
"gnomad_genomes_af": 0.0000131387,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9987785220146179,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "CardioboostCm",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.94,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9709,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.774,
"phylop100way_prediction": "Benign",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PS4,PM2,PP3",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PS4",
"PM2",
"PP3"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000355349.4",
"gene_symbol": "MYH7",
"hgnc_id": 7577,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.4258C>T",
"hgvs_p": "p.Arg1420Trp"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NR_126491.1",
"gene_symbol": "MHRT",
"hgnc_id": 51291,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*3G>A",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive, myosin storage,6 conditions,Cardiomyopathy,Cardiovascular phenotype,Dilated cardiomyopathy 1S,Hypertrophic cardiomyopathy,Hypertrophic cardiomyopathy 1,MYH7-related skeletal myopathy,Myopathy,Myosin storage myopathy,Primary familial hypertrophic cardiomyopathy,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:6 LP:12",
"phenotype_combined": "Primary familial hypertrophic cardiomyopathy|Hypertrophic cardiomyopathy|Myosin storage myopathy|not provided|Cardiomyopathy|Cardiovascular phenotype|6 conditions|Dilated cardiomyopathy 1S|Hypertrophic cardiomyopathy 1|MYH7-related skeletal myopathy|Myopathy, myosin storage, autosomal recessive|MYH7-related skeletal myopathy;Hypertrophic cardiomyopathy 1;Dilated cardiomyopathy 1S;Myopathy, myosin storage, autosomal recessive;Myosin storage myopathy",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}