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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: 5-127396639-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=127396639&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 127396639,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001256545.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "NM_001256545.2",
"protein_id": "NP_001243474.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 1140,
"cds_start": 520,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 7606,
"mane_select": "ENST00000503335.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "ENST00000503335.7",
"protein_id": "ENSP00000423354.2",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 1140,
"cds_start": 520,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 7606,
"mane_select": "NM_001256545.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "ENST00000274473.6",
"protein_id": "ENSP00000274473.6",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 1140,
"cds_start": 520,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 787,
"cdna_end": null,
"cdna_length": 7594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "ENST00000418761.6",
"protein_id": "ENSP00000416284.2",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 567,
"cds_start": 520,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 2238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "ENST00000508365.5",
"protein_id": "ENSP00000423195.1",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 567,
"cds_start": 520,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 749,
"cdna_end": null,
"cdna_length": 2365,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "NM_032446.3",
"protein_id": "NP_115822.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 1140,
"cds_start": 520,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 7657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "NM_001308119.2",
"protein_id": "NP_001295048.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 567,
"cds_start": 520,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 2466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "NM_001308121.2",
"protein_id": "NP_001295050.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 567,
"cds_start": 520,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 2415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.685C>A",
"hgvs_p": "p.Arg229Arg",
"transcript": "XM_017009987.2",
"protein_id": "XP_016865476.1",
"transcript_support_level": null,
"aa_start": 229,
"aa_end": null,
"aa_length": 1195,
"cds_start": 685,
"cds_end": null,
"cds_length": 3588,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 8153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg",
"transcript": "XM_011543694.1",
"protein_id": "XP_011541996.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 1140,
"cds_start": 520,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 594,
"cdna_end": null,
"cdna_length": 7401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"dbsnp": "rs756799749",
"frequency_reference_population": 0.0000061572814,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000615728,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.27000001072883606,
"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": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.126,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_001256545.2",
"gene_symbol": "MEGF10",
"hgnc_id": 29634,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.520C>A",
"hgvs_p": "p.Arg174Arg"
}
],
"clinvar_disease": "MEGF10-related myopathy",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "MEGF10-related myopathy",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}