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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: 12-50248679-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=50248679&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 50248679,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000341247.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_016357.5",
"protein_id": "NP_057441.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 759,
"cds_start": 73,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 197,
"cdna_end": null,
"cdna_length": 3680,
"mane_select": "ENST00000341247.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "ENST00000341247.9",
"protein_id": "ENSP00000340184.4",
"transcript_support_level": 1,
"aa_start": 25,
"aa_end": null,
"aa_length": 759,
"cds_start": 73,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 197,
"cdna_end": null,
"cdna_length": 3680,
"mane_select": "NM_016357.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "ENST00000394943.7",
"protein_id": "ENSP00000378400.3",
"transcript_support_level": 1,
"aa_start": 25,
"aa_end": null,
"aa_length": 760,
"cds_start": 73,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 183,
"cdna_end": null,
"cdna_length": 3669,
"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": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "n.73C>A",
"hgvs_p": null,
"transcript": "ENST00000552720.5",
"protein_id": "ENSP00000448411.1",
"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": 2457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001113546.2",
"protein_id": "NP_001107018.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 760,
"cds_start": 73,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 197,
"cdna_end": null,
"cdna_length": 3683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001394886.1",
"protein_id": "NP_001381815.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 760,
"cds_start": 73,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 349,
"cdna_end": null,
"cdna_length": 3835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001394887.1",
"protein_id": "NP_001381816.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 759,
"cds_start": 73,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 301,
"cdna_end": null,
"cdna_length": 3784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001394888.1",
"protein_id": "NP_001381817.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 759,
"cds_start": 73,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 349,
"cdna_end": null,
"cdna_length": 3832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001394889.1",
"protein_id": "NP_001381818.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 759,
"cds_start": 73,
"cds_end": null,
"cds_length": 2280,
"cdna_start": 197,
"cdna_end": null,
"cdna_length": 3680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001394890.1",
"protein_id": "NP_001381819.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 758,
"cds_start": 73,
"cds_end": null,
"cds_length": 2277,
"cdna_start": 197,
"cdna_end": null,
"cdna_length": 3677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001394891.1",
"protein_id": "NP_001381820.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 742,
"cds_start": 73,
"cds_end": null,
"cds_length": 2229,
"cdna_start": 197,
"cdna_end": null,
"cdna_length": 3629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001394892.1",
"protein_id": "NP_001381821.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 682,
"cds_start": 73,
"cds_end": null,
"cds_length": 2049,
"cdna_start": 197,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "NM_001394893.1",
"protein_id": "NP_001381822.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 668,
"cds_start": 73,
"cds_end": null,
"cds_length": 2007,
"cdna_start": 197,
"cdna_end": null,
"cdna_length": 3407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "ENST00000551691.5",
"protein_id": "ENSP00000447975.1",
"transcript_support_level": 3,
"aa_start": 25,
"aa_end": null,
"aa_length": 129,
"cds_start": 73,
"cds_end": null,
"cds_length": 391,
"cdna_start": 265,
"cdna_end": null,
"cdna_length": 583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile",
"transcript": "ENST00000550592.1",
"protein_id": "ENSP00000449890.1",
"transcript_support_level": 4,
"aa_start": 25,
"aa_end": null,
"aa_length": 110,
"cds_start": 73,
"cds_end": null,
"cds_length": 333,
"cdna_start": 307,
"cdna_end": null,
"cdna_length": 567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LIMA1",
"gene_hgnc_id": 24636,
"dbsnp": "rs140372565",
"frequency_reference_population": 0.00007559872,
"hom_count_reference_population": 0,
"allele_count_reference_population": 122,
"gnomad_exomes_af": 0.0000738989,
"gnomad_genomes_af": 0.0000919069,
"gnomad_exomes_ac": 108,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01256212592124939,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.287,
"revel_prediction": "Benign",
"alphamissense_score": 0.1126,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.311,
"phylop100way_prediction": "Uncertain_significance",
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000341247.9",
"gene_symbol": "LIMA1",
"hgnc_id": 24636,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.73C>A",
"hgvs_p": "p.Leu25Ile"
}
],
"clinvar_disease": "LOW DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 8",
"clinvar_classification": "association",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "LOW DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 8",
"pathogenicity_classification_combined": "association",
"custom_annotations": null
}
],
"message": null
}