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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: 19-54510541-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=54510541&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "LAIR2",
"hgnc_id": 6478,
"hgvs_c": "c.431C>T",
"hgvs_p": "p.Thr144Ile",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_002288.6",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 18,
"alphamissense_prediction": null,
"alphamissense_score": 0.1709,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.09416985511779785,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 152,
"aa_ref": "T",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 665,
"cdna_start": 519,
"cds_end": null,
"cds_length": 459,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_002288.6",
"gene_hgnc_id": 6478,
"gene_symbol": "LAIR2",
"hgvs_c": "c.431C>T",
"hgvs_p": "p.Thr144Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000301202.7",
"protein_coding": true,
"protein_id": "NP_002279.2",
"strand": true,
"transcript": "NM_002288.6",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 152,
"aa_ref": "T",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 665,
"cdna_start": 519,
"cds_end": null,
"cds_length": 459,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000301202.7",
"gene_hgnc_id": 6478,
"gene_symbol": "LAIR2",
"hgvs_c": "c.431C>T",
"hgvs_p": "p.Thr144Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002288.6",
"protein_coding": true,
"protein_id": "ENSP00000301202.2",
"strand": true,
"transcript": "ENST00000301202.7",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 135,
"aa_ref": "T",
"aa_start": 127,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 538,
"cdna_start": 392,
"cds_end": null,
"cds_length": 408,
"cds_start": 380,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000351841.2",
"gene_hgnc_id": 6478,
"gene_symbol": "LAIR2",
"hgvs_c": "c.380C>T",
"hgvs_p": "p.Thr127Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000301203.2",
"strand": true,
"transcript": "ENST00000351841.2",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 140,
"aa_ref": "T",
"aa_start": 132,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 650,
"cdna_start": 535,
"cds_end": null,
"cds_length": 423,
"cds_start": 395,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000956664.1",
"gene_hgnc_id": 6478,
"gene_symbol": "LAIR2",
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Thr132Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626723.1",
"strand": true,
"transcript": "ENST00000956664.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 135,
"aa_ref": "T",
"aa_start": 127,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 614,
"cdna_start": 468,
"cds_end": null,
"cds_length": 408,
"cds_start": 380,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_021270.5",
"gene_hgnc_id": 6478,
"gene_symbol": "LAIR2",
"hgvs_c": "c.380C>T",
"hgvs_p": "p.Thr127Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_067154.1",
"strand": true,
"transcript": "NM_021270.5",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 140,
"aa_ref": "T",
"aa_start": 132,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 629,
"cdna_start": 483,
"cds_end": null,
"cds_length": 423,
"cds_start": 395,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011526961.3",
"gene_hgnc_id": 6478,
"gene_symbol": "LAIR2",
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Thr132Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525263.1",
"strand": true,
"transcript": "XM_011526961.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs562511626",
"effect": "missense_variant",
"frequency_reference_population": 0.000011155887,
"gene_hgnc_id": 6478,
"gene_symbol": "LAIR2",
"gnomad_exomes_ac": 15,
"gnomad_exomes_af": 0.0000102646,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197163,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.022,
"pos": 54510541,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.032,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002288.6"
}
]
}