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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: 5-127455461-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=127455461&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 127455461,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000503335.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.3086C>T",
"hgvs_p": "p.Pro1029Leu",
"transcript": "NM_001256545.2",
"protein_id": "NP_001243474.1",
"transcript_support_level": null,
"aa_start": 1029,
"aa_end": null,
"aa_length": 1140,
"cds_start": 3086,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 3365,
"cdna_end": null,
"cdna_length": 7606,
"mane_select": "ENST00000503335.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.3086C>T",
"hgvs_p": "p.Pro1029Leu",
"transcript": "ENST00000503335.7",
"protein_id": "ENSP00000423354.2",
"transcript_support_level": 1,
"aa_start": 1029,
"aa_end": null,
"aa_length": 1140,
"cds_start": 3086,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 3365,
"cdna_end": null,
"cdna_length": 7606,
"mane_select": "NM_001256545.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.3086C>T",
"hgvs_p": "p.Pro1029Leu",
"transcript": "ENST00000274473.6",
"protein_id": "ENSP00000274473.6",
"transcript_support_level": 1,
"aa_start": 1029,
"aa_end": null,
"aa_length": 1140,
"cds_start": 3086,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 3353,
"cdna_end": null,
"cdna_length": 7594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.3086C>T",
"hgvs_p": "p.Pro1029Leu",
"transcript": "NM_032446.3",
"protein_id": "NP_115822.1",
"transcript_support_level": null,
"aa_start": 1029,
"aa_end": null,
"aa_length": 1140,
"cds_start": 3086,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 3416,
"cdna_end": null,
"cdna_length": 7657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.3251C>T",
"hgvs_p": "p.Pro1084Leu",
"transcript": "XM_017009987.2",
"protein_id": "XP_016865476.1",
"transcript_support_level": null,
"aa_start": 1084,
"aa_end": null,
"aa_length": 1195,
"cds_start": 3251,
"cds_end": null,
"cds_length": 3588,
"cdna_start": 3912,
"cdna_end": null,
"cdna_length": 8153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.3086C>T",
"hgvs_p": "p.Pro1029Leu",
"transcript": "XM_011543694.1",
"protein_id": "XP_011541996.1",
"transcript_support_level": null,
"aa_start": 1029,
"aa_end": null,
"aa_length": 1140,
"cds_start": 3086,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 3160,
"cdna_end": null,
"cdna_length": 7401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.1946C>T",
"hgvs_p": "p.Pro649Leu",
"transcript": "XM_017009988.2",
"protein_id": "XP_016865477.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 760,
"cds_start": 1946,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 6347,
"cdna_end": null,
"cdna_length": 10588,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "n.585C>T",
"hgvs_p": null,
"transcript": "ENST00000510828.5",
"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": 686,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "n.287C>T",
"hgvs_p": null,
"transcript": "ENST00000515622.1",
"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": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"dbsnp": "rs139251235",
"frequency_reference_population": 0.000030359995,
"hom_count_reference_population": 0,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000328352,
"gnomad_genomes_af": 0.00000657384,
"gnomad_exomes_ac": 48,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8841100931167603,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.717,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7482,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"phylop100way_prediction": "Pathogenic",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000503335.7",
"gene_symbol": "MEGF10",
"hgnc_id": 29634,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3086C>T",
"hgvs_p": "p.Pro1029Leu"
}
],
"clinvar_disease": "MEGF10-related myopathy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "MEGF10-related myopathy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}