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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: 3-134951699-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=134951699&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 134951699,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004441.5",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "c.452T>C",
"hgvs_p": "p.Phe151Ser",
"transcript": "NM_004441.5",
"protein_id": "NP_004432.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 984,
"cds_start": 452,
"cds_end": null,
"cds_length": 2955,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000398015.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004441.5"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "c.452T>C",
"hgvs_p": "p.Phe151Ser",
"transcript": "ENST00000398015.8",
"protein_id": "ENSP00000381097.3",
"transcript_support_level": 1,
"aa_start": 151,
"aa_end": null,
"aa_length": 984,
"cds_start": 452,
"cds_end": null,
"cds_length": 2955,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004441.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000398015.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "n.452T>C",
"hgvs_p": null,
"transcript": "ENST00000482618.5",
"protein_id": "ENSP00000420338.1",
"transcript_support_level": 1,
"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": "nonsense_mediated_decay",
"feature": "ENST00000482618.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "n.452T>C",
"hgvs_p": null,
"transcript": "ENST00000488154.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "pseudogene",
"feature": "ENST00000488154.5"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "c.452T>C",
"hgvs_p": "p.Phe151Ser",
"transcript": "ENST00000647596.1",
"protein_id": "ENSP00000497153.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 1055,
"cds_start": 452,
"cds_end": null,
"cds_length": 3168,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647596.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "c.452T>C",
"hgvs_p": "p.Phe151Ser",
"transcript": "ENST00000970111.1",
"protein_id": "ENSP00000640170.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 943,
"cds_start": 452,
"cds_end": null,
"cds_length": 2832,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970111.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "c.452T>C",
"hgvs_p": "p.Phe151Ser",
"transcript": "ENST00000895120.1",
"protein_id": "ENSP00000565179.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 912,
"cds_start": 452,
"cds_end": null,
"cds_length": 2739,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000895120.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "c.452T>C",
"hgvs_p": "p.Phe151Ser",
"transcript": "ENST00000928305.1",
"protein_id": "ENSP00000598364.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 830,
"cds_start": 452,
"cds_end": null,
"cds_length": 2493,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928305.1"
},
{
"aa_ref": "F",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "c.386T>C",
"hgvs_p": "p.Phe129Ser",
"transcript": "ENST00000474732.1",
"protein_id": "ENSP00000418352.1",
"transcript_support_level": 4,
"aa_start": 129,
"aa_end": null,
"aa_length": 148,
"cds_start": 386,
"cds_end": null,
"cds_length": 449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000474732.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"hgvs_c": "c.*78T>C",
"hgvs_p": null,
"transcript": "ENST00000473867.5",
"protein_id": "ENSP00000417216.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 101,
"cds_start": null,
"cds_end": null,
"cds_length": 308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000473867.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288700",
"gene_hgnc_id": null,
"hgvs_c": "n.*48T>C",
"hgvs_p": null,
"transcript": "ENST00000460895.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000460895.5"
}
],
"gene_symbol": "EPHB1",
"gene_hgnc_id": 3392,
"dbsnp": "rs140725416",
"frequency_reference_population": 0.0000018588305,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000136815,
"gnomad_genomes_af": 0.00000657505,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4561489522457123,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.298,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9099,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.223,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.06,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004441.5",
"gene_symbol": "EPHB1",
"hgnc_id": 3392,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.452T>C",
"hgvs_p": "p.Phe151Ser"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000460895.5",
"gene_symbol": "ENSG00000288700",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*48T>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}