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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: 1-179882863-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=179882863&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TOR1AIP1",
"hgnc_id": 29456,
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Glu121Lys",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_001267578.2",
"verdict": "Likely_benign"
},
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "TOR1AIP2",
"hgnc_id": 24055,
"hgvs_c": "c.-327C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "ENST00000894825.1",
"verdict": "Likely_benign"
},
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000272906",
"hgnc_id": null,
"hgvs_c": "n.-160C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -3,
"transcript": "ENST00000610272.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6",
"acmg_score": -3,
"allele_count_reference_population": 264,
"alphamissense_prediction": null,
"alphamissense_score": 0.1459,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2Y,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.034744828939437866,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 583,
"aa_ref": "E",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3807,
"cdna_start": 579,
"cds_end": null,
"cds_length": 1752,
"cds_start": 361,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_015602.4",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Glu121Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000606911.7",
"protein_coding": true,
"protein_id": "NP_056417.2",
"strand": true,
"transcript": "NM_015602.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 583,
"aa_ref": "E",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3807,
"cdna_start": 579,
"cds_end": null,
"cds_length": 1752,
"cds_start": 361,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000606911.7",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Glu121Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015602.4",
"protein_coding": true,
"protein_id": "ENSP00000476687.1",
"strand": true,
"transcript": "ENST00000606911.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 462,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3397,
"cdna_start": null,
"cds_end": null,
"cds_length": 1389,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000435319.8",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "c.-3G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000393292.3",
"strand": true,
"transcript": "ENST00000435319.8",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 599,
"aa_ref": "E",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3044,
"cdna_start": 567,
"cds_end": null,
"cds_length": 1800,
"cds_start": 361,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000271583.7",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Glu121Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000271583.3",
"strand": true,
"transcript": "ENST00000271583.7",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 584,
"aa_ref": "E",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3810,
"cdna_start": 579,
"cds_end": null,
"cds_length": 1755,
"cds_start": 361,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001267578.2",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Glu121Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001254507.1",
"strand": true,
"transcript": "NM_001267578.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 584,
"aa_ref": "E",
"aa_start": 121,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3685,
"cdna_start": 822,
"cds_end": null,
"cds_length": 1755,
"cds_start": 361,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000528443.6",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "c.361G>A",
"hgvs_p": "p.Glu121Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000435365.2",
"strand": true,
"transcript": "ENST00000528443.6",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 192,
"aa_ref": "E",
"aa_start": 24,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 579,
"cdna_start": 70,
"cds_end": null,
"cds_length": 579,
"cds_start": 70,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000531630.6",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "c.70G>A",
"hgvs_p": "p.Glu24Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000434316.2",
"strand": true,
"transcript": "ENST00000531630.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 470,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2445,
"cdna_start": null,
"cds_end": null,
"cds_length": 1413,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000894825.1",
"gene_hgnc_id": 24055,
"gene_symbol": "TOR1AIP2",
"hgvs_c": "c.-327C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000564884.1",
"strand": false,
"transcript": "ENST00000894825.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 470,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4472,
"cdna_start": null,
"cds_end": null,
"cds_length": 1413,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000936116.1",
"gene_hgnc_id": 24055,
"gene_symbol": "TOR1AIP2",
"hgvs_c": "c.-761C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606175.1",
"strand": false,
"transcript": "ENST00000936116.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 470,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4462,
"cdna_start": null,
"cds_end": null,
"cds_length": 1413,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000942404.1",
"gene_hgnc_id": 24055,
"gene_symbol": "TOR1AIP2",
"hgvs_c": "c.-746C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612463.1",
"strand": false,
"transcript": "ENST00000942404.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 196,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 593,
"cdna_start": null,
"cds_end": null,
"cds_length": 592,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000527391.5",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "c.-27G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000432717.1",
"strand": true,
"transcript": "ENST00000527391.5",
"transcript_support_level": 5
},
{
"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": 587,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000529091.5",
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"hgvs_c": "n.-105G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000433759.1",
"strand": true,
"transcript": "ENST00000529091.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1097,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 1,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000610272.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000272906",
"hgvs_c": "n.-160C>T",
"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": "ENST00000610272.2",
"transcript_support_level": 6
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199933063",
"effect": "missense_variant",
"frequency_reference_population": 0.00016354526,
"gene_hgnc_id": 29456,
"gene_symbol": "TOR1AIP1",
"gnomad_exomes_ac": 240,
"gnomad_exomes_af": 0.000164172,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 24,
"gnomad_genomes_af": 0.000157534,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2Y|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.503,
"pos": 179882863,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.172,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001267578.2"
}
]
}