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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: 1-179889339-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=179889339&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 179889339,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000606911.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194Cys",
"transcript": "NM_015602.4",
"protein_id": "NP_056417.2",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 583,
"cds_start": 580,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 798,
"cdna_end": null,
"cdna_length": 3807,
"mane_select": "ENST00000606911.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194Cys",
"transcript": "ENST00000606911.7",
"protein_id": "ENSP00000476687.1",
"transcript_support_level": 1,
"aa_start": 194,
"aa_end": null,
"aa_length": 583,
"cds_start": 580,
"cds_end": null,
"cds_length": 1752,
"cdna_start": 798,
"cdna_end": null,
"cdna_length": 3807,
"mane_select": "NM_015602.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.217C>T",
"hgvs_p": "p.Arg73Cys",
"transcript": "ENST00000435319.8",
"protein_id": "ENSP00000393292.3",
"transcript_support_level": 1,
"aa_start": 73,
"aa_end": null,
"aa_length": 462,
"cds_start": 217,
"cds_end": null,
"cds_length": 1389,
"cdna_start": 387,
"cdna_end": null,
"cdna_length": 3397,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.Arg195Cys",
"transcript": "ENST00000271583.7",
"protein_id": "ENSP00000271583.3",
"transcript_support_level": 5,
"aa_start": 195,
"aa_end": null,
"aa_length": 599,
"cds_start": 583,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 789,
"cdna_end": null,
"cdna_length": 3044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.Arg195Cys",
"transcript": "NM_001267578.2",
"protein_id": "NP_001254507.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 584,
"cds_start": 583,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 801,
"cdna_end": null,
"cdna_length": 3810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.583C>T",
"hgvs_p": "p.Arg195Cys",
"transcript": "ENST00000528443.6",
"protein_id": "ENSP00000435365.2",
"transcript_support_level": 2,
"aa_start": 195,
"aa_end": null,
"aa_length": 584,
"cds_start": 583,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 1044,
"cdna_end": null,
"cdna_length": 3685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.208C>T",
"hgvs_p": "p.Arg70Cys",
"transcript": "ENST00000527391.5",
"protein_id": "ENSP00000432717.1",
"transcript_support_level": 5,
"aa_start": 70,
"aa_end": null,
"aa_length": 196,
"cds_start": 208,
"cds_end": null,
"cds_length": 592,
"cdna_start": 209,
"cdna_end": null,
"cdna_length": 593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "c.289C>T",
"hgvs_p": "p.Arg97Cys",
"transcript": "ENST00000531630.6",
"protein_id": "ENSP00000434316.2",
"transcript_support_level": 5,
"aa_start": 97,
"aa_end": null,
"aa_length": 192,
"cds_start": 289,
"cds_end": null,
"cds_length": 579,
"cdna_start": 289,
"cdna_end": null,
"cdna_length": 579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "n.172C>T",
"hgvs_p": null,
"transcript": "ENST00000474875.5",
"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": 830,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "n.149C>T",
"hgvs_p": null,
"transcript": "ENST00000524653.1",
"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": 544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "n.328C>T",
"hgvs_p": null,
"transcript": "ENST00000527867.5",
"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": 486,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "n.*180C>T",
"hgvs_p": null,
"transcript": "ENST00000529091.5",
"protein_id": "ENSP00000433759.1",
"transcript_support_level": 4,
"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": 587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "n.169C>T",
"hgvs_p": null,
"transcript": "ENST00000531726.5",
"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": 475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"hgvs_c": "n.*180C>T",
"hgvs_p": null,
"transcript": "ENST00000529091.5",
"protein_id": "ENSP00000433759.1",
"transcript_support_level": 4,
"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": 587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TOR1AIP1",
"gene_hgnc_id": 29456,
"dbsnp": "rs534816625",
"frequency_reference_population": 0.000037326245,
"hom_count_reference_population": 0,
"allele_count_reference_population": 60,
"gnomad_exomes_af": 0.0000247385,
"gnomad_genomes_af": 0.000157662,
"gnomad_exomes_ac": 36,
"gnomad_genomes_ac": 24,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01120084524154663,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.14000000059604645,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.079,
"revel_prediction": "Benign",
"alphamissense_score": 0.0647,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.55,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.14,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000606911.7",
"gene_symbol": "TOR1AIP1",
"hgnc_id": 29456,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194Cys"
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2Y,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": "Autosomal recessive limb-girdle muscular dystrophy type 2Y|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}