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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: 10-62813710-AGGC-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=62813710&ref=AGGC&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 62813710,
"ref": "AGGC",
"alt": "A",
"effect": "conservative_inframe_deletion",
"transcript": "ENST00000242480.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.925_927delGCC",
"hgvs_p": "p.Ala309del",
"transcript": "NM_000399.5",
"protein_id": "NP_000390.2",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 476,
"cds_start": 925,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 2979,
"mane_select": "ENST00000242480.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.925_927delGCC",
"hgvs_p": "p.Ala309del",
"transcript": "ENST00000242480.4",
"protein_id": "ENSP00000242480.3",
"transcript_support_level": 1,
"aa_start": 309,
"aa_end": null,
"aa_length": 476,
"cds_start": 925,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 2979,
"mane_select": "NM_000399.5",
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "n.*940_*942delGCC",
"hgvs_p": null,
"transcript": "ENST00000439032.6",
"protein_id": "ENSP00000509775.1",
"transcript_support_level": 1,
"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": 3155,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "n.*940_*942delGCC",
"hgvs_p": null,
"transcript": "ENST00000439032.6",
"protein_id": "ENSP00000509775.1",
"transcript_support_level": 1,
"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": 3155,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.964_966delGCC",
"hgvs_p": "p.Ala322del",
"transcript": "NM_001410931.1",
"protein_id": "NP_001397860.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 489,
"cds_start": 964,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 1102,
"cdna_end": null,
"cdna_length": 2817,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.964_966delGCC",
"hgvs_p": "p.Ala322del",
"transcript": "ENST00000691610.1",
"protein_id": "ENSP00000509830.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 489,
"cds_start": 964,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 986,
"cdna_end": null,
"cdna_length": 1490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.925_927delGCC",
"hgvs_p": "p.Ala309del",
"transcript": "NM_001136177.3",
"protein_id": "NP_001129649.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 476,
"cds_start": 925,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 1081,
"cdna_end": null,
"cdna_length": 2796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.925_927delGCC",
"hgvs_p": "p.Ala309del",
"transcript": "NM_001136178.2",
"protein_id": "NP_001129650.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 476,
"cds_start": 925,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 1136,
"cdna_end": null,
"cdna_length": 2851,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.925_927delGCC",
"hgvs_p": "p.Ala309del",
"transcript": "ENST00000637191.2",
"protein_id": "ENSP00000490154.2",
"transcript_support_level": 4,
"aa_start": 309,
"aa_end": null,
"aa_length": 476,
"cds_start": 925,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 1081,
"cdna_end": null,
"cdna_length": 2796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.775_777delGCC",
"hgvs_p": "p.Ala259del",
"transcript": "NM_001136179.3",
"protein_id": "NP_001129651.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 426,
"cds_start": 775,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 1164,
"cdna_end": null,
"cdna_length": 2879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.775_777delGCC",
"hgvs_p": "p.Ala259del",
"transcript": "NM_001321037.2",
"protein_id": "NP_001307966.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 426,
"cds_start": 775,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 981,
"cdna_end": null,
"cdna_length": 2696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "c.775_777delGCC",
"hgvs_p": "p.Ala259del",
"transcript": "ENST00000411732.4",
"protein_id": "ENSP00000387634.1",
"transcript_support_level": 2,
"aa_start": 259,
"aa_end": null,
"aa_length": 426,
"cds_start": 775,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 1171,
"cdna_end": null,
"cdna_length": 2882,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "n.*857_*859delGCC",
"hgvs_p": null,
"transcript": "ENST00000690143.1",
"protein_id": "ENSP00000510306.1",
"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": 1640,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "n.*857_*859delGCC",
"hgvs_p": null,
"transcript": "ENST00000690143.1",
"protein_id": "ENSP00000510306.1",
"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": 1640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"hgvs_c": "n.109-751_109-749delGCC",
"hgvs_p": null,
"transcript": "ENST00000639815.1",
"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": 1075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EGR2",
"gene_hgnc_id": 3239,
"dbsnp": "rs753747037",
"frequency_reference_population": 0.000060819097,
"hom_count_reference_population": 0,
"allele_count_reference_population": 98,
"gnomad_exomes_af": 0.0000603036,
"gnomad_genomes_af": 0.0000657661,
"gnomad_exomes_ac": 88,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.185,
"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": "PM4_Supporting,BP6,BS1",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PM4_Supporting",
"BP6",
"BS1"
],
"verdict": "Likely_benign",
"transcript": "ENST00000242480.4",
"gene_symbol": "EGR2",
"hgnc_id": 3239,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.925_927delGCC",
"hgvs_p": "p.Ala309del"
}
],
"clinvar_disease": " type I,Charcot-Marie-Tooth disease,EGR2-related disorder,Inborn genetic diseases",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Charcot-Marie-Tooth disease, type I|Inborn genetic diseases|EGR2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}