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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: 5-128328749-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=128328749&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 128328749,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001999.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "c.4418G>A",
"hgvs_p": "p.Arg1473His",
"transcript": "NM_001999.4",
"protein_id": "NP_001990.2",
"transcript_support_level": null,
"aa_start": 1473,
"aa_end": null,
"aa_length": 2912,
"cds_start": 4418,
"cds_end": null,
"cds_length": 8739,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000262464.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001999.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "c.4418G>A",
"hgvs_p": "p.Arg1473His",
"transcript": "ENST00000262464.9",
"protein_id": "ENSP00000262464.4",
"transcript_support_level": 1,
"aa_start": 1473,
"aa_end": null,
"aa_length": 2912,
"cds_start": 4418,
"cds_end": null,
"cds_length": 8739,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001999.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262464.9"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "c.4319G>A",
"hgvs_p": "p.Arg1440His",
"transcript": "ENST00000939405.1",
"protein_id": "ENSP00000609464.1",
"transcript_support_level": null,
"aa_start": 1440,
"aa_end": null,
"aa_length": 2879,
"cds_start": 4319,
"cds_end": null,
"cds_length": 8640,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939405.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "c.4265G>A",
"hgvs_p": "p.Arg1422His",
"transcript": "ENST00000939404.1",
"protein_id": "ENSP00000609463.1",
"transcript_support_level": null,
"aa_start": 1422,
"aa_end": null,
"aa_length": 2861,
"cds_start": 4265,
"cds_end": null,
"cds_length": 8586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939404.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "c.4319G>A",
"hgvs_p": "p.Arg1440His",
"transcript": "ENST00000508989.5",
"protein_id": "ENSP00000425596.1",
"transcript_support_level": 2,
"aa_start": 1440,
"aa_end": null,
"aa_length": 1473,
"cds_start": 4319,
"cds_end": null,
"cds_length": 4422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000508989.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "c.4265G>A",
"hgvs_p": "p.Arg1422His",
"transcript": "XM_017009228.3",
"protein_id": "XP_016864717.1",
"transcript_support_level": null,
"aa_start": 1422,
"aa_end": null,
"aa_length": 2861,
"cds_start": 4265,
"cds_end": null,
"cds_length": 8586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009228.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "n.1205G>A",
"hgvs_p": null,
"transcript": "ENST00000507835.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000507835.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "n.1202G>A",
"hgvs_p": null,
"transcript": "ENST00000703783.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000703783.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "n.1283G>A",
"hgvs_p": null,
"transcript": "ENST00000703785.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000703785.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"hgvs_c": "n.1024G>A",
"hgvs_p": null,
"transcript": "ENST00000703786.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000703786.1"
}
],
"gene_symbol": "FBN2",
"gene_hgnc_id": 3604,
"dbsnp": "rs140812463",
"frequency_reference_population": 0.00004708868,
"hom_count_reference_population": 0,
"allele_count_reference_population": 76,
"gnomad_exomes_af": 0.0000485697,
"gnomad_genomes_af": 0.0000328601,
"gnomad_exomes_ac": 71,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.735345184803009,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.678,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.0909,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.994,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001999.4",
"gene_symbol": "FBN2",
"hgnc_id": 3604,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4418G>A",
"hgvs_p": "p.Arg1473His"
}
],
"clinvar_disease": "Congenital contractural arachnodactyly,Ehlers-Danlos syndrome,Familial thoracic aortic aneurysm and aortic dissection,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 B:1",
"phenotype_combined": "not provided|not specified|Congenital contractural arachnodactyly|Ehlers-Danlos syndrome|Familial thoracic aortic aneurysm and aortic dissection",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}