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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: 16-46707704-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=46707704&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM4"
],
"effects": [
"stop_lost"
],
"gene_symbol": "MYLK3",
"hgnc_id": 29826,
"hgvs_c": "c.2460A>C",
"hgvs_p": "p.Ter820Tyrext*?",
"inheritance_mode": "AD,AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_182493.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM4",
"acmg_score": 4,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.05,
"chr": "16",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": -0.05000000074505806,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 819,
"aa_ref": "*",
"aa_start": 820,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8033,
"cdna_start": 2611,
"cds_end": null,
"cds_length": 2460,
"cds_start": 2460,
"consequences": [
"stop_lost"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_182493.3",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "c.2460A>C",
"hgvs_p": "p.Ter820Tyrext*?",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000394809.9",
"protein_coding": true,
"protein_id": "NP_872299.2",
"strand": false,
"transcript": "NM_182493.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 819,
"aa_ref": "*",
"aa_start": 820,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8033,
"cdna_start": 2611,
"cds_end": null,
"cds_length": 2460,
"cds_start": 2460,
"consequences": [
"stop_lost"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000394809.9",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "c.2460A>C",
"hgvs_p": "p.Ter820Tyrext*?",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_182493.3",
"protein_coding": true,
"protein_id": "ENSP00000378288.4",
"strand": false,
"transcript": "ENST00000394809.9",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 820,
"aa_ref": "*",
"aa_start": 821,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4024,
"cdna_start": 2614,
"cds_end": null,
"cds_length": 2463,
"cds_start": 2463,
"consequences": [
"stop_lost"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000874186.1",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "c.2463A>C",
"hgvs_p": "p.Ter821Tyrext*?",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544245.1",
"strand": false,
"transcript": "ENST00000874186.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 819,
"aa_ref": "*",
"aa_start": 820,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2736,
"cdna_start": 2641,
"cds_end": null,
"cds_length": 2460,
"cds_start": 2460,
"consequences": [
"stop_lost"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000874187.1",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "c.2460A>C",
"hgvs_p": "p.Ter820Tyrext*?",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000544246.1",
"strand": false,
"transcript": "ENST00000874187.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 811,
"aa_ref": "*",
"aa_start": 812,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4024,
"cdna_start": 2632,
"cds_end": null,
"cds_length": 2436,
"cds_start": 2436,
"consequences": [
"stop_lost"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000971334.1",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "c.2436A>C",
"hgvs_p": "p.Ter812Tyrext*?",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000641393.1",
"strand": false,
"transcript": "ENST00000971334.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 478,
"aa_ref": "*",
"aa_start": 479,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7179,
"cdna_start": 1757,
"cds_end": null,
"cds_length": 1437,
"cds_start": 1437,
"consequences": [
"stop_lost"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001308301.1",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "c.1437A>C",
"hgvs_p": "p.Ter479Tyrext*?",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001295230.1",
"strand": false,
"transcript": "NM_001308301.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 478,
"aa_ref": "*",
"aa_start": 479,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1795,
"cdna_start": 1757,
"cds_end": null,
"cds_length": 1437,
"cds_start": 1437,
"consequences": [
"stop_lost"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000536476.5",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "c.1437A>C",
"hgvs_p": "p.Ter479Tyrext*?",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000439297.1",
"strand": false,
"transcript": "ENST00000536476.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 562,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000562104.1",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "n.550A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000562104.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 580,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000565182.5",
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"hgvs_c": "n.544A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000565182.5",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "stop_lost",
"frequency_reference_population": null,
"gene_hgnc_id": 29826,
"gene_symbol": "MYLK3",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.757,
"pos": 46707704,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_182493.3"
}
]
}