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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: 5-170248735-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=170248735&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 170248735,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_005565.5",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCP2",
"gene_hgnc_id": 6529,
"hgvs_c": "c.1564T>C",
"hgvs_p": "p.Tyr522His",
"transcript": "NM_005565.5",
"protein_id": "NP_005556.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 533,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000046794.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005565.5"
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCP2",
"gene_hgnc_id": 6529,
"hgvs_c": "c.1564T>C",
"hgvs_p": "p.Tyr522His",
"transcript": "ENST00000046794.10",
"protein_id": "ENSP00000046794.5",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 533,
"cds_start": 1564,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005565.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000046794.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "C5orf58",
"gene_hgnc_id": 37272,
"hgvs_c": "c.95-2913A>G",
"hgvs_p": null,
"transcript": "ENST00000524171.5",
"protein_id": "ENSP00000490552.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 33,
"cds_start": null,
"cds_end": null,
"cds_length": 102,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000524171.5"
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCP2",
"gene_hgnc_id": 6529,
"hgvs_c": "c.1573T>C",
"hgvs_p": "p.Tyr525His",
"transcript": "ENST00000968849.1",
"protein_id": "ENSP00000638908.1",
"transcript_support_level": null,
"aa_start": 525,
"aa_end": null,
"aa_length": 536,
"cds_start": 1573,
"cds_end": null,
"cds_length": 1611,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968849.1"
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCP2",
"gene_hgnc_id": 6529,
"hgvs_c": "c.1480T>C",
"hgvs_p": "p.Tyr494His",
"transcript": "ENST00000968850.1",
"protein_id": "ENSP00000638909.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 505,
"cds_start": 1480,
"cds_end": null,
"cds_length": 1518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968850.1"
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCP2",
"gene_hgnc_id": 6529,
"hgvs_c": "c.949T>C",
"hgvs_p": "p.Tyr317His",
"transcript": "ENST00000521416.5",
"protein_id": "ENSP00000428871.1",
"transcript_support_level": 2,
"aa_start": 317,
"aa_end": null,
"aa_length": 328,
"cds_start": 949,
"cds_end": null,
"cds_length": 987,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000521416.5"
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCP2",
"gene_hgnc_id": 6529,
"hgvs_c": "c.1333T>C",
"hgvs_p": "p.Tyr445His",
"transcript": "XM_047417171.1",
"protein_id": "XP_047273127.1",
"transcript_support_level": null,
"aa_start": 445,
"aa_end": null,
"aa_length": 456,
"cds_start": 1333,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417171.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "C5orf58",
"gene_hgnc_id": 37272,
"hgvs_c": "c.95-2913A>G",
"hgvs_p": null,
"transcript": "ENST00000517575.4",
"protein_id": "ENSP00000490661.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 33,
"cds_start": null,
"cds_end": null,
"cds_length": 102,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000517575.4"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LCP2",
"gene_hgnc_id": 6529,
"hgvs_c": "n.1048T>C",
"hgvs_p": null,
"transcript": "ENST00000520322.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000520322.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "C5orf58",
"gene_hgnc_id": 37272,
"hgvs_c": "n.202-2913A>G",
"hgvs_p": null,
"transcript": "NR_131091.3",
"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_131091.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "C5orf58",
"gene_hgnc_id": 37272,
"hgvs_c": "n.118-2913A>G",
"hgvs_p": null,
"transcript": "NR_131092.3",
"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_131092.3"
}
],
"gene_symbol": "LCP2",
"gene_hgnc_id": 6529,
"dbsnp": "rs187889192",
"frequency_reference_population": 0.0032782082,
"hom_count_reference_population": 15,
"allele_count_reference_population": 5280,
"gnomad_exomes_af": 0.00334417,
"gnomad_genomes_af": 0.00264648,
"gnomad_exomes_ac": 4877,
"gnomad_genomes_ac": 403,
"gnomad_exomes_homalt": 13,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0057239830493927,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.106,
"revel_prediction": "Benign",
"alphamissense_score": 0.1911,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.082,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005565.5",
"gene_symbol": "LCP2",
"hgnc_id": 6529,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1564T>C",
"hgvs_p": "p.Tyr522His"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000524171.5",
"gene_symbol": "C5orf58",
"hgnc_id": 37272,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.95-2913A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}