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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: 1-30735210-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=30735210&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 30735210,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_006762.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "c.662C>T",
"hgvs_p": "p.Ser221Leu",
"transcript": "NM_006762.3",
"protein_id": "NP_006753.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 262,
"cds_start": 662,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000294507.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006762.3"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "c.662C>T",
"hgvs_p": "p.Ser221Leu",
"transcript": "ENST00000294507.4",
"protein_id": "ENSP00000294507.3",
"transcript_support_level": 1,
"aa_start": 221,
"aa_end": null,
"aa_length": 262,
"cds_start": 662,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006762.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000294507.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "c.695C>T",
"hgvs_p": "p.Ser232Leu",
"transcript": "ENST00000875065.1",
"protein_id": "ENSP00000545124.1",
"transcript_support_level": null,
"aa_start": 232,
"aa_end": null,
"aa_length": 273,
"cds_start": 695,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875065.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "c.662C>T",
"hgvs_p": "p.Ser221Leu",
"transcript": "ENST00000875064.1",
"protein_id": "ENSP00000545123.1",
"transcript_support_level": null,
"aa_start": 221,
"aa_end": null,
"aa_length": 270,
"cds_start": 662,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875064.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "c.647C>T",
"hgvs_p": "p.Ser216Leu",
"transcript": "ENST00000875063.1",
"protein_id": "ENSP00000545122.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 257,
"cds_start": 647,
"cds_end": null,
"cds_length": 774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875063.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "c.491C>T",
"hgvs_p": "p.Ser164Leu",
"transcript": "ENST00000875062.1",
"protein_id": "ENSP00000545121.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 205,
"cds_start": 491,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875062.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "c.443C>T",
"hgvs_p": "p.Ser148Leu",
"transcript": "ENST00000953433.1",
"protein_id": "ENSP00000623492.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 189,
"cds_start": 443,
"cds_end": null,
"cds_length": 570,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953433.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "c.491C>T",
"hgvs_p": "p.Ser164Leu",
"transcript": "XM_011542098.3",
"protein_id": "XP_011540400.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 205,
"cds_start": 491,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011542098.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"hgvs_c": "n.887C>T",
"hgvs_p": null,
"transcript": "ENST00000464569.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000464569.1"
}
],
"gene_symbol": "LAPTM5",
"gene_hgnc_id": 29612,
"dbsnp": "rs761225896",
"frequency_reference_population": 0.00002394518,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000239452,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 35,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08856907486915588,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.059,
"revel_prediction": "Benign",
"alphamissense_score": 0.0679,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.556,
"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_006762.3",
"gene_symbol": "LAPTM5",
"hgnc_id": 29612,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.662C>T",
"hgvs_p": "p.Ser221Leu"
}
],
"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
}