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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: 19-12649146-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12649146&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 12649146,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000456935.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.2426T>C",
"hgvs_p": "p.Leu809Pro",
"transcript": "NM_000528.4",
"protein_id": "NP_000519.2",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 1011,
"cds_start": 2426,
"cds_end": null,
"cds_length": 3036,
"cdna_start": 2467,
"cdna_end": null,
"cdna_length": 3185,
"mane_select": "ENST00000456935.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.2426T>C",
"hgvs_p": "p.Leu809Pro",
"transcript": "ENST00000456935.7",
"protein_id": "ENSP00000395473.2",
"transcript_support_level": 1,
"aa_start": 809,
"aa_end": null,
"aa_length": 1011,
"cds_start": 2426,
"cds_end": null,
"cds_length": 3036,
"cdna_start": 2467,
"cdna_end": null,
"cdna_length": 3185,
"mane_select": "NM_000528.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.2423T>C",
"hgvs_p": "p.Leu808Pro",
"transcript": "ENST00000221363.9",
"protein_id": "ENSP00000221363.4",
"transcript_support_level": 1,
"aa_start": 808,
"aa_end": null,
"aa_length": 1010,
"cds_start": 2423,
"cds_end": null,
"cds_length": 3033,
"cdna_start": 2456,
"cdna_end": null,
"cdna_length": 5855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.2429T>C",
"hgvs_p": "p.Leu810Pro",
"transcript": "NM_001440570.1",
"protein_id": "NP_001427499.1",
"transcript_support_level": null,
"aa_start": 810,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2429,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 2470,
"cdna_end": null,
"cdna_length": 3188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.2423T>C",
"hgvs_p": "p.Leu808Pro",
"transcript": "NM_001173498.2",
"protein_id": "NP_001166969.1",
"transcript_support_level": null,
"aa_start": 808,
"aa_end": null,
"aa_length": 1010,
"cds_start": 2423,
"cds_end": null,
"cds_length": 3033,
"cdna_start": 2464,
"cdna_end": null,
"cdna_length": 3182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.1325T>C",
"hgvs_p": "p.Leu442Pro",
"transcript": "XM_047438841.1",
"protein_id": "XP_047294797.1",
"transcript_support_level": null,
"aa_start": 442,
"aa_end": null,
"aa_length": 644,
"cds_start": 1325,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 1430,
"cdna_end": null,
"cdna_length": 2148,
"mane_select": null,
"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": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "n.3016T>C",
"hgvs_p": null,
"transcript": "ENST00000466794.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 3685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"dbsnp": "rs80338681",
"frequency_reference_population": 0.000088708686,
"hom_count_reference_population": 0,
"allele_count_reference_population": 143,
"gnomad_exomes_af": 0.0000924745,
"gnomad_genomes_af": 0.0000525776,
"gnomad_exomes_ac": 135,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9561733603477478,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.829,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8657,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.42,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.793,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM1",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000456935.7",
"gene_symbol": "MAN2B1",
"hgnc_id": 6826,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2426T>C",
"hgvs_p": "p.Leu809Pro"
}
],
"clinvar_disease": "Deficiency of alpha-mannosidase,MAN2B1-related disorder",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:1 O:1",
"phenotype_combined": "Deficiency of alpha-mannosidase|MAN2B1-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}