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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: 3-184276991-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=184276991&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "EEF1AKMT4-ECE2",
"hgnc_id": 53615,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Gly194Ser",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_014693.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 5,
"criteria": [
"BP4",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ECE2",
"hgnc_id": 13275,
"hgvs_c": "c.364G>A",
"hgvs_p": "p.Gly122Ser",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -5,
"transcript": "NM_001100120.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 9,
"alphamissense_prediction": null,
"alphamissense_score": 0.1063,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.31,
"chr": "3",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.28643739223480225,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 765,
"aa_ref": "G",
"aa_start": 76,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": 358,
"cds_end": null,
"cds_length": 2298,
"cds_start": 226,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001100121.2",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Gly76Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000404464.8",
"protein_coding": true,
"protein_id": "NP_001093591.1",
"strand": true,
"transcript": "NM_001100121.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 765,
"aa_ref": "G",
"aa_start": 76,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": 358,
"cds_end": null,
"cds_length": 2298,
"cds_start": 226,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000404464.8",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Gly76Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001100121.2",
"protein_coding": true,
"protein_id": "ENSP00000385846.3",
"strand": true,
"transcript": "ENST00000404464.8",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 883,
"aa_ref": "G",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3445,
"cdna_start": 580,
"cds_end": null,
"cds_length": 2652,
"cds_start": 580,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000402825.7",
"gene_hgnc_id": 53615,
"gene_symbol": "EEF1AKMT4-ECE2",
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Gly194Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384223.3",
"strand": true,
"transcript": "ENST00000402825.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 811,
"aa_ref": "G",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2667,
"cdna_start": 483,
"cds_end": null,
"cds_length": 2436,
"cds_start": 364,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000357474.9",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.364G>A",
"hgvs_p": "p.Gly122Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000350066.5",
"strand": true,
"transcript": "ENST00000357474.9",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 736,
"aa_ref": "G",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3147,
"cdna_start": 282,
"cds_end": null,
"cds_length": 2211,
"cds_start": 139,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000359140.8",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Gly47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000352052.4",
"strand": true,
"transcript": "ENST00000359140.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1961,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000490579.1",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "n.62G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000490579.1",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 883,
"aa_ref": "G",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3468,
"cdna_start": 603,
"cds_end": null,
"cds_length": 2652,
"cds_start": 580,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_014693.4",
"gene_hgnc_id": 53615,
"gene_symbol": "EEF1AKMT4-ECE2",
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Gly194Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_055508.3",
"strand": true,
"transcript": "NM_014693.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 811,
"aa_ref": "G",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3361,
"cdna_start": 496,
"cds_end": null,
"cds_length": 2436,
"cds_start": 364,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001100120.2",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.364G>A",
"hgvs_p": "p.Gly122Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001093590.1",
"strand": true,
"transcript": "NM_001100120.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 811,
"aa_ref": "G",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3365,
"cdna_start": 501,
"cds_end": null,
"cds_length": 2436,
"cds_start": 364,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000949185.1",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.364G>A",
"hgvs_p": "p.Gly122Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619244.1",
"strand": true,
"transcript": "ENST00000949185.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 774,
"aa_ref": "G",
"aa_start": 122,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3238,
"cdna_start": 486,
"cds_end": null,
"cds_length": 2325,
"cds_start": 364,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000855515.1",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.364G>A",
"hgvs_p": "p.Gly122Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525574.1",
"strand": true,
"transcript": "ENST00000855515.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 736,
"aa_ref": "G",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3136,
"cdna_start": 271,
"cds_end": null,
"cds_length": 2211,
"cds_start": 139,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001037324.3",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Gly47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001032401.1",
"strand": true,
"transcript": "NM_001037324.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 716,
"aa_ref": "G",
"aa_start": 68,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2588,
"cdna_start": 202,
"cds_end": null,
"cds_length": 2151,
"cds_start": 202,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000430587.1",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.202G>A",
"hgvs_p": "p.Gly68Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000398444.1",
"strand": true,
"transcript": "ENST00000430587.1",
"transcript_support_level": 2
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 714,
"aa_ref": "G",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3072,
"cdna_start": 274,
"cds_end": null,
"cds_length": 2145,
"cds_start": 139,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000949186.1",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Gly47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619245.1",
"strand": true,
"transcript": "ENST00000949186.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 709,
"aa_ref": "G",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2923,
"cdna_start": 139,
"cds_end": null,
"cds_length": 2130,
"cds_start": 139,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000855516.1",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Gly47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525575.1",
"strand": true,
"transcript": "ENST00000855516.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 660,
"aa_ref": "G",
"aa_start": 47,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2902,
"cdna_start": 265,
"cds_end": null,
"cds_length": 1983,
"cds_start": 139,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000855514.1",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "c.139G>A",
"hgvs_p": "p.Gly47Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525573.1",
"strand": true,
"transcript": "ENST00000855514.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 588,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000422932.5",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "n.139G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000392467.1",
"strand": true,
"transcript": "ENST00000422932.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 572,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000474750.1",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "n.220G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000474750.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2277,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000488401.5",
"gene_hgnc_id": 13275,
"gene_symbol": "ECE2",
"hgvs_c": "n.265G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000488401.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1246132620",
"effect": "missense_variant",
"frequency_reference_population": 0.0000061567844,
"gene_hgnc_id": 53615,
"gene_symbol": "EEF1AKMT4-ECE2",
"gnomad_exomes_ac": 9,
"gnomad_exomes_af": 0.00000615678,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.471,
"pos": 184276991,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.155,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_014693.4"
}
]
}