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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: 18-2547479-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=2547479&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 2547479,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_022840.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "S",
"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": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Leu317Ser",
"transcript": "NM_022840.5",
"protein_id": "NP_073751.3",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 472,
"cds_start": 950,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 3684,
"mane_select": "ENST00000574538.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": true,
"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": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Leu317Ser",
"transcript": "ENST00000574538.2",
"protein_id": "ENSP00000458290.1",
"transcript_support_level": 1,
"aa_start": 317,
"aa_end": null,
"aa_length": 472,
"cds_start": 950,
"cds_end": null,
"cds_length": 1419,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 3684,
"mane_select": "NM_022840.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "n.3251T>C",
"hgvs_p": null,
"transcript": "ENST00000573134.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Leu317Ser",
"transcript": "NM_001308401.2",
"protein_id": "NP_001295330.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 419,
"cds_start": 950,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 3592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Leu317Ser",
"transcript": "ENST00000319888.10",
"protein_id": "ENSP00000320349.6",
"transcript_support_level": 5,
"aa_start": 317,
"aa_end": null,
"aa_length": 419,
"cds_start": 950,
"cds_end": null,
"cds_length": 1260,
"cdna_start": 1749,
"cdna_end": null,
"cdna_length": 3601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.143T>C",
"hgvs_p": "p.Leu48Ser",
"transcript": "ENST00000576251.5",
"protein_id": "ENSP00000460774.1",
"transcript_support_level": 2,
"aa_start": 48,
"aa_end": null,
"aa_length": 91,
"cds_start": 143,
"cds_end": null,
"cds_length": 276,
"cdna_start": 145,
"cdna_end": null,
"cdna_length": 1884,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"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": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Leu317Ser",
"transcript": "XM_047437741.1",
"protein_id": "XP_047293697.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 449,
"cds_start": 950,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 2263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Leu317Ser",
"transcript": "XM_005258132.5",
"protein_id": "XP_005258189.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 360,
"cds_start": 950,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 3485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"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": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.509T>C",
"hgvs_p": "p.Leu170Ser",
"transcript": "XM_005258133.4",
"protein_id": "XP_005258190.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 325,
"cds_start": 509,
"cds_end": null,
"cds_length": 978,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "METTL4",
"gene_hgnc_id": 24726,
"hgvs_c": "c.899+5216T>C",
"hgvs_p": null,
"transcript": "XM_011525730.4",
"protein_id": "XP_011524032.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 325,
"cds_start": -4,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3310,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "METTL4",
"gene_hgnc_id": 24726,
"dbsnp": "rs753042888",
"frequency_reference_population": 0.0000037239972,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000274173,
"gnomad_genomes_af": 0.0000131372,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9377384781837463,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.584,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9192,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.259,
"phylop100way_prediction": "Pathogenic",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_022840.5",
"gene_symbol": "METTL4",
"hgnc_id": 24726,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.950T>C",
"hgvs_p": "p.Leu317Ser"
}
],
"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
}