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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: 6-31572779-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31572779&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 31572779,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000595.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"hgvs_c": "c.37T>C",
"hgvs_p": "p.Cys13Arg",
"transcript": "NM_000595.4",
"protein_id": "NP_000586.2",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 205,
"cds_start": 37,
"cds_end": null,
"cds_length": 618,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 1416,
"mane_select": "ENST00000418386.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000595.4"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"hgvs_c": "c.37T>C",
"hgvs_p": "p.Cys13Arg",
"transcript": "ENST00000418386.3",
"protein_id": "ENSP00000413450.2",
"transcript_support_level": 1,
"aa_start": 13,
"aa_end": null,
"aa_length": 205,
"cds_start": 37,
"cds_end": null,
"cds_length": 618,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 1416,
"mane_select": "NM_000595.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000418386.3"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"hgvs_c": "c.37T>C",
"hgvs_p": "p.Cys13Arg",
"transcript": "NM_001159740.2",
"protein_id": "NP_001153212.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 205,
"cds_start": 37,
"cds_end": null,
"cds_length": 618,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 1462,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001159740.2"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"hgvs_c": "c.37T>C",
"hgvs_p": "p.Cys13Arg",
"transcript": "ENST00000454783.5",
"protein_id": "ENSP00000403495.1",
"transcript_support_level": 2,
"aa_start": 13,
"aa_end": null,
"aa_length": 205,
"cds_start": 37,
"cds_end": null,
"cds_length": 618,
"cdna_start": 295,
"cdna_end": null,
"cdna_length": 1507,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000454783.5"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"hgvs_c": "c.37T>C",
"hgvs_p": "p.Cys13Arg",
"transcript": "ENST00000877327.1",
"protein_id": "ENSP00000547386.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 205,
"cds_start": 37,
"cds_end": null,
"cds_length": 618,
"cdna_start": 310,
"cdna_end": null,
"cdna_length": 1522,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877327.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"hgvs_c": "c.37T>C",
"hgvs_p": "p.Cys13Arg",
"transcript": "XM_047418773.1",
"protein_id": "XP_047274729.1",
"transcript_support_level": null,
"aa_start": 13,
"aa_end": null,
"aa_length": 205,
"cds_start": 37,
"cds_end": null,
"cds_length": 618,
"cdna_start": 1038,
"cdna_end": null,
"cdna_length": 2250,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418773.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"hgvs_c": "n.199T>C",
"hgvs_p": null,
"transcript": "ENST00000471842.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1497,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000471842.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"hgvs_c": "n.79T>C",
"hgvs_p": null,
"transcript": "ENST00000489638.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 1377,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000489638.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289406",
"gene_hgnc_id": null,
"hgvs_c": "n.3A>G",
"hgvs_p": null,
"transcript": "ENST00000691266.2",
"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": 1105,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000691266.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC100287329",
"gene_hgnc_id": null,
"hgvs_c": "n.-76A>G",
"hgvs_p": null,
"transcript": "NR_149045.1",
"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": 1273,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_149045.1"
}
],
"gene_symbol": "LTA",
"gene_hgnc_id": 6709,
"dbsnp": "rs2229094",
"frequency_reference_population": 0.26298767,
"hom_count_reference_population": 56590,
"allele_count_reference_population": 423286,
"gnomad_exomes_af": 0.262112,
"gnomad_genomes_af": 0.271428,
"gnomad_exomes_ac": 382238,
"gnomad_genomes_ac": 41048,
"gnomad_exomes_homalt": 50970,
"gnomad_genomes_homalt": 5620,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005508542060852051,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.20000000298023224,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.037,
"revel_prediction": "Benign",
"alphamissense_score": 0.0443,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.598,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.2,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000595.4",
"gene_symbol": "LTA",
"hgnc_id": 6709,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.37T>C",
"hgvs_p": "p.Cys13Arg"
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000691266.2",
"gene_symbol": "ENSG00000289406",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3A>G",
"hgvs_p": null
},
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "NR_149045.1",
"gene_symbol": "LOC100287329",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-76A>G",
"hgvs_p": null
}
],
"clinvar_disease": "LTA-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "LTA-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}