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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: 19-48493945-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48493945&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 48493945,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001080434.2",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.3841G>A",
"hgvs_p": "p.Glu1281Lys",
"transcript": "NM_001388485.1",
"protein_id": "NP_001375414.1",
"transcript_support_level": null,
"aa_start": 1281,
"aa_end": null,
"aa_length": 1460,
"cds_start": 3841,
"cds_end": null,
"cds_length": 4383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000600059.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001388485.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.3841G>A",
"hgvs_p": "p.Glu1281Lys",
"transcript": "ENST00000600059.6",
"protein_id": "ENSP00000472020.1",
"transcript_support_level": 2,
"aa_start": 1281,
"aa_end": null,
"aa_length": 1460,
"cds_start": 3841,
"cds_end": null,
"cds_length": 4383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001388485.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600059.6"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.3919G>A",
"hgvs_p": "p.Glu1307Lys",
"transcript": "ENST00000650440.1",
"protein_id": "ENSP00000497480.1",
"transcript_support_level": null,
"aa_start": 1307,
"aa_end": null,
"aa_length": 1486,
"cds_start": 3919,
"cds_end": null,
"cds_length": 4461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000650440.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.3841G>A",
"hgvs_p": "p.Glu1281Lys",
"transcript": "NM_001080434.2",
"protein_id": "NP_001073903.2",
"transcript_support_level": null,
"aa_start": 1281,
"aa_end": null,
"aa_length": 1460,
"cds_start": 3841,
"cds_end": null,
"cds_length": 4383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001080434.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.3841G>A",
"hgvs_p": "p.Glu1281Lys",
"transcript": "ENST00000673139.1",
"protein_id": "ENSP00000500153.1",
"transcript_support_level": null,
"aa_start": 1281,
"aa_end": null,
"aa_length": 1460,
"cds_start": 3841,
"cds_end": null,
"cds_length": 4383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000673139.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.3106G>A",
"hgvs_p": "p.Glu1036Lys",
"transcript": "ENST00000672160.1",
"protein_id": "ENSP00000500093.1",
"transcript_support_level": null,
"aa_start": 1036,
"aa_end": null,
"aa_length": 1215,
"cds_start": 3106,
"cds_end": null,
"cds_length": 3648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000672160.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.1178G>A",
"hgvs_p": "p.Arg393Gln",
"transcript": "ENST00000648216.1",
"protein_id": "ENSP00000497855.1",
"transcript_support_level": null,
"aa_start": 393,
"aa_end": null,
"aa_length": 650,
"cds_start": 1178,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000648216.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.3919G>A",
"hgvs_p": "p.Glu1307Lys",
"transcript": "XM_011526411.3",
"protein_id": "XP_011524713.1",
"transcript_support_level": null,
"aa_start": 1307,
"aa_end": null,
"aa_length": 1486,
"cds_start": 3919,
"cds_end": null,
"cds_length": 4461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526411.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"hgvs_c": "c.3886G>A",
"hgvs_p": "p.Glu1296Lys",
"transcript": "XM_011526412.3",
"protein_id": "XP_011524714.1",
"transcript_support_level": null,
"aa_start": 1296,
"aa_end": null,
"aa_length": 1475,
"cds_start": 3886,
"cds_end": null,
"cds_length": 4428,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011526412.3"
}
],
"gene_symbol": "LMTK3",
"gene_hgnc_id": 19295,
"dbsnp": "rs1252250550",
"frequency_reference_population": 0.000017356591,
"hom_count_reference_population": 0,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000168696,
"gnomad_genomes_af": 0.0000202848,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.21356451511383057,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.228,
"revel_prediction": "Benign",
"alphamissense_score": 0.3254,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.64,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001080434.2",
"gene_symbol": "LMTK3",
"hgnc_id": 19295,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3841G>A",
"hgvs_p": "p.Glu1281Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}