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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: 6-106279773-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=106279773&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 106279773,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000369076.8",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.366A>T",
"hgvs_p": "p.Glu122Asp",
"transcript": "NM_004849.4",
"protein_id": "NP_004840.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 275,
"cds_start": 366,
"cds_end": null,
"cds_length": 828,
"cdna_start": 659,
"cdna_end": null,
"cdna_length": 3185,
"mane_select": "ENST00000369076.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.366A>T",
"hgvs_p": "p.Glu122Asp",
"transcript": "ENST00000369076.8",
"protein_id": "ENSP00000358072.3",
"transcript_support_level": 1,
"aa_start": 122,
"aa_end": null,
"aa_length": 275,
"cds_start": 366,
"cds_end": null,
"cds_length": 828,
"cdna_start": 659,
"cdna_end": null,
"cdna_length": 3185,
"mane_select": "NM_004849.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.366A>T",
"hgvs_p": "p.Glu122Asp",
"transcript": "ENST00000343245.7",
"protein_id": "ENSP00000343313.3",
"transcript_support_level": 1,
"aa_start": 122,
"aa_end": null,
"aa_length": 275,
"cds_start": 366,
"cds_end": null,
"cds_length": 828,
"cdna_start": 566,
"cdna_end": null,
"cdna_length": 3092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.132A>T",
"hgvs_p": "p.Glu44Asp",
"transcript": "ENST00000635758.2",
"protein_id": "ENSP00000490493.1",
"transcript_support_level": 1,
"aa_start": 44,
"aa_end": null,
"aa_length": 197,
"cds_start": 132,
"cds_end": null,
"cds_length": 594,
"cdna_start": 509,
"cdna_end": null,
"cdna_length": 3035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"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": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.366A>T",
"hgvs_p": "p.Glu122Asp",
"transcript": "ENST00000613993.1",
"protein_id": "ENSP00000483135.1",
"transcript_support_level": 1,
"aa_start": 122,
"aa_end": null,
"aa_length": 162,
"cds_start": 366,
"cds_end": null,
"cds_length": 489,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 733,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "n.*103A>T",
"hgvs_p": null,
"transcript": "ENST00000369070.5",
"protein_id": "ENSP00000358066.2",
"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": 3088,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "n.*103A>T",
"hgvs_p": null,
"transcript": "ENST00000369070.5",
"protein_id": "ENSP00000358066.2",
"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": 3088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.109-31529A>T",
"hgvs_p": null,
"transcript": "ENST00000360666.6",
"protein_id": "ENSP00000353884.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 91,
"cds_start": -4,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.366A>T",
"hgvs_p": "p.Glu122Asp",
"transcript": "NM_001286106.2",
"protein_id": "NP_001273035.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 275,
"cds_start": 366,
"cds_end": null,
"cds_length": 828,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 3112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.366A>T",
"hgvs_p": "p.Glu122Asp",
"transcript": "NM_001286108.2",
"protein_id": "NP_001273037.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 213,
"cds_start": 366,
"cds_end": null,
"cds_length": 642,
"cdna_start": 659,
"cdna_end": null,
"cdna_length": 3181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.132A>T",
"hgvs_p": "p.Glu44Asp",
"transcript": "NM_001286107.2",
"protein_id": "NP_001273036.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 197,
"cds_start": 132,
"cds_end": null,
"cds_length": 594,
"cdna_start": 531,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.132A>T",
"hgvs_p": "p.Glu44Asp",
"transcript": "ENST00000636437.1",
"protein_id": "ENSP00000490376.1",
"transcript_support_level": 5,
"aa_start": 44,
"aa_end": null,
"aa_length": 153,
"cds_start": 132,
"cds_end": null,
"cds_length": 462,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 2261,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.366A>T",
"hgvs_p": "p.Glu122Asp",
"transcript": "XM_047419573.1",
"protein_id": "XP_047275529.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 233,
"cds_start": 366,
"cds_end": null,
"cds_length": 702,
"cdna_start": 659,
"cdna_end": null,
"cdna_length": 1004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.156A>T",
"hgvs_p": "p.Glu52Asp",
"transcript": "XM_047419574.1",
"protein_id": "XP_047275530.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 205,
"cds_start": 156,
"cds_end": null,
"cds_length": 618,
"cdna_start": 674,
"cdna_end": null,
"cdna_length": 3200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.132A>T",
"hgvs_p": "p.Glu44Asp",
"transcript": "XM_024446590.2",
"protein_id": "XP_024302358.1",
"transcript_support_level": null,
"aa_start": 44,
"aa_end": null,
"aa_length": 197,
"cds_start": 132,
"cds_end": null,
"cds_length": 594,
"cdna_start": 458,
"cdna_end": null,
"cdna_length": 2984,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "n.51A>T",
"hgvs_p": null,
"transcript": "ENST00000476518.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 602,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "n.132A>T",
"hgvs_p": null,
"transcript": "ENST00000636335.1",
"protein_id": "ENSP00000490221.1",
"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": 1219,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "n.366A>T",
"hgvs_p": null,
"transcript": "ENST00000646025.1",
"protein_id": "ENSP00000495958.1",
"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": 1888,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "n.424A>T",
"hgvs_p": null,
"transcript": "NR_104402.1",
"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": 2855,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "n.296A>T",
"hgvs_p": null,
"transcript": "NR_104403.1",
"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": 2727,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"hgvs_c": "c.109-31529A>T",
"hgvs_p": null,
"transcript": "NM_001286111.2",
"protein_id": "NP_001273040.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 91,
"cds_start": -4,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATG5",
"gene_hgnc_id": 589,
"dbsnp": "rs1131692265",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8790755271911621,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.72,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.92,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.542,
"phylop100way_prediction": "Benign",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000369076.8",
"gene_symbol": "ATG5",
"hgnc_id": 589,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.366A>T",
"hgvs_p": "p.Glu122Asp"
}
],
"clinvar_disease": " autosomal recessive 25,Spinocerebellar ataxia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Spinocerebellar ataxia, autosomal recessive 25",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}