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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: 2-77518919-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=77518919&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 77518919,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001330370.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.950G>T",
"hgvs_p": "p.Arg317Leu",
"transcript": "NM_001134745.3",
"protein_id": "NP_001128217.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 590,
"cds_start": 950,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000409884.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001134745.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.950G>T",
"hgvs_p": "p.Arg317Leu",
"transcript": "ENST00000409884.6",
"protein_id": "ENSP00000387297.1",
"transcript_support_level": 1,
"aa_start": 317,
"aa_end": null,
"aa_length": 590,
"cds_start": 950,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001134745.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409884.6"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.953G>T",
"hgvs_p": "p.Arg318Leu",
"transcript": "ENST00000409282.1",
"protein_id": "ENSP00000386286.1",
"transcript_support_level": 1,
"aa_start": 318,
"aa_end": null,
"aa_length": 519,
"cds_start": 953,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409282.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.950G>T",
"hgvs_p": "p.Arg317Leu",
"transcript": "ENST00000409088.3",
"protein_id": "ENSP00000386236.3",
"transcript_support_level": 1,
"aa_start": 317,
"aa_end": null,
"aa_length": 518,
"cds_start": 950,
"cds_end": null,
"cds_length": 1557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409088.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.953G>T",
"hgvs_p": "p.Arg318Leu",
"transcript": "NM_001330370.2",
"protein_id": "NP_001317299.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 591,
"cds_start": 953,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330370.2"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.953G>T",
"hgvs_p": "p.Arg318Leu",
"transcript": "ENST00000409911.5",
"protein_id": "ENSP00000387228.1",
"transcript_support_level": 5,
"aa_start": 318,
"aa_end": null,
"aa_length": 591,
"cds_start": 953,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409911.5"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.950G>T",
"hgvs_p": "p.Arg317Leu",
"transcript": "NM_001282924.3",
"protein_id": "NP_001269853.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 590,
"cds_start": 950,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282924.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.950G>T",
"hgvs_p": "p.Arg317Leu",
"transcript": "ENST00000409093.1",
"protein_id": "ENSP00000386357.1",
"transcript_support_level": 2,
"aa_start": 317,
"aa_end": null,
"aa_length": 590,
"cds_start": 950,
"cds_end": null,
"cds_length": 1773,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409093.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.953G>T",
"hgvs_p": "p.Arg318Leu",
"transcript": "NM_001282928.3",
"protein_id": "NP_001269857.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 519,
"cds_start": 953,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282928.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "c.950G>T",
"hgvs_p": "p.Arg317Leu",
"transcript": "NM_024993.6",
"protein_id": "NP_079269.4",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 518,
"cds_start": 950,
"cds_end": null,
"cds_length": 1557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024993.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"hgvs_c": "n.268+3190G>T",
"hgvs_p": null,
"transcript": "NR_146416.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_146416.2"
}
],
"gene_symbol": "LRRTM4",
"gene_hgnc_id": 19411,
"dbsnp": "rs762478440",
"frequency_reference_population": 0.0000020598002,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.0000020598,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1620720624923706,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.088,
"revel_prediction": "Benign",
"alphamissense_score": 0.2213,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.369,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001330370.2",
"gene_symbol": "LRRTM4",
"hgnc_id": 19411,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.953G>T",
"hgvs_p": "p.Arg318Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}