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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: 2-55871091-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=55871091&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 55871091,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000355426.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "c.1033C>T",
"hgvs_p": "p.Arg345Trp",
"transcript": "NM_001039348.3",
"protein_id": "NP_001034437.1",
"transcript_support_level": null,
"aa_start": 345,
"aa_end": null,
"aa_length": 493,
"cds_start": 1033,
"cds_end": null,
"cds_length": 1482,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 2708,
"mane_select": "ENST00000355426.8",
"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": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "c.1033C>T",
"hgvs_p": "p.Arg345Trp",
"transcript": "ENST00000355426.8",
"protein_id": "ENSP00000347596.3",
"transcript_support_level": 1,
"aa_start": 345,
"aa_end": null,
"aa_length": 493,
"cds_start": 1033,
"cds_end": null,
"cds_length": 1482,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 2708,
"mane_select": "NM_001039348.3",
"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": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "c.1033C>T",
"hgvs_p": "p.Arg345Trp",
"transcript": "ENST00000394555.6",
"protein_id": "ENSP00000378058.2",
"transcript_support_level": 1,
"aa_start": 345,
"aa_end": null,
"aa_length": 493,
"cds_start": 1033,
"cds_end": null,
"cds_length": 1482,
"cdna_start": 1469,
"cdna_end": null,
"cdna_length": 3024,
"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": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "c.1033C>T",
"hgvs_p": "p.Arg345Trp",
"transcript": "NM_001039349.3",
"protein_id": "NP_001034438.1",
"transcript_support_level": null,
"aa_start": 345,
"aa_end": null,
"aa_length": 493,
"cds_start": 1033,
"cds_end": null,
"cds_length": 1482,
"cdna_start": 1112,
"cdna_end": null,
"cdna_length": 2667,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "c.391C>T",
"hgvs_p": "p.Arg131Trp",
"transcript": "ENST00000634374.1",
"protein_id": "ENSP00000489183.1",
"transcript_support_level": 5,
"aa_start": 131,
"aa_end": null,
"aa_length": 279,
"cds_start": 391,
"cds_end": null,
"cds_length": 840,
"cdna_start": 392,
"cdna_end": null,
"cdna_length": 1007,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "c.793C>T",
"hgvs_p": "p.Arg265Trp",
"transcript": "XM_005264205.5",
"protein_id": "XP_005264262.2",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 413,
"cds_start": 793,
"cds_end": null,
"cds_length": 1242,
"cdna_start": 913,
"cdna_end": null,
"cdna_length": 2468,
"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": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "c.793C>T",
"hgvs_p": "p.Arg265Trp",
"transcript": "XM_017003586.3",
"protein_id": "XP_016859075.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 413,
"cds_start": 793,
"cds_end": null,
"cds_length": 1242,
"cdna_start": 872,
"cdna_end": null,
"cdna_length": 2427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "n.*685C>T",
"hgvs_p": null,
"transcript": "ENST00000635671.1",
"protein_id": "ENSP00000489578.1",
"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": 1809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"hgvs_c": "n.*685C>T",
"hgvs_p": null,
"transcript": "ENST00000635671.1",
"protein_id": "ENSP00000489578.1",
"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": 1809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC112268416",
"gene_hgnc_id": null,
"hgvs_c": "n.229-2792G>A",
"hgvs_p": null,
"transcript": "XR_002959388.2",
"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": 383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EFEMP1",
"gene_hgnc_id": 3218,
"dbsnp": "rs121434491",
"frequency_reference_population": 0.000012316771,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000123168,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 18,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8964512348175049,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.27000001072883606,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.709,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3567,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.966,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.27,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000355426.8",
"gene_symbol": "EFEMP1",
"hgnc_id": 3218,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1033C>T",
"hgvs_p": "p.Arg345Trp"
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XR_002959388.2",
"gene_symbol": "LOC112268416",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.229-2792G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Doyne honeycomb retinal dystrophy,Retinal dystrophy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1",
"phenotype_combined": "not provided|Doyne honeycomb retinal dystrophy|Retinal dystrophy",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}