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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: 5-109712432-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=109712432&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MAN2A1",
"hgnc_id": 6824,
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_002372.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 15020,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.89,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8899999856948853,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1144,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6553,
"cdna_start": null,
"cds_end": null,
"cds_length": 3435,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_002372.4",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000261483.5",
"protein_coding": true,
"protein_id": "NP_002363.2",
"strand": true,
"transcript": "NM_002372.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1144,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6553,
"cdna_start": null,
"cds_end": null,
"cds_length": 3435,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000261483.5",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002372.4",
"protein_coding": true,
"protein_id": "ENSP00000261483.4",
"strand": true,
"transcript": "ENST00000261483.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1148,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4633,
"cdna_start": null,
"cds_end": null,
"cds_length": 3447,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880526.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550585.1",
"strand": true,
"transcript": "ENST00000880526.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1143,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4633,
"cdna_start": null,
"cds_end": null,
"cds_length": 3432,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000968351.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638410.1",
"strand": true,
"transcript": "ENST00000968351.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1142,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4652,
"cdna_start": null,
"cds_end": null,
"cds_length": 3429,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880524.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550583.1",
"strand": true,
"transcript": "ENST00000880524.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1116,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3716,
"cdna_start": null,
"cds_end": null,
"cds_length": 3351,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000968353.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638412.1",
"strand": true,
"transcript": "ENST00000968353.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6431,
"cdna_start": null,
"cds_end": null,
"cds_length": 3312,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000929782.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599841.1",
"strand": true,
"transcript": "ENST00000929782.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1097,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4500,
"cdna_start": null,
"cds_end": null,
"cds_length": 3294,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880525.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550584.1",
"strand": true,
"transcript": "ENST00000880525.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1083,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3801,
"cdna_start": null,
"cds_end": null,
"cds_length": 3252,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880527.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550586.1",
"strand": true,
"transcript": "ENST00000880527.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1080,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4428,
"cdna_start": null,
"cds_end": null,
"cds_length": 3243,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000929783.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000599842.1",
"strand": true,
"transcript": "ENST00000929783.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1071,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3926,
"cdna_start": null,
"cds_end": null,
"cds_length": 3216,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000968352.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000638411.1",
"strand": true,
"transcript": "ENST00000968352.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1052,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6806,
"cdna_start": null,
"cds_end": null,
"cds_length": 3159,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880523.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550582.1",
"strand": true,
"transcript": "ENST00000880523.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1095,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5948,
"cdna_start": null,
"cds_end": null,
"cds_length": 3288,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017009472.2",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.-12-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864961.1",
"strand": true,
"transcript": "XM_017009472.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 884,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3204,
"cdna_start": null,
"cds_end": null,
"cds_length": 2655,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011543395.4",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "c.136-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011541697.1",
"strand": true,
"transcript": "XM_011543395.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2647,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007058604.1",
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"hgvs_c": "n.627-1088C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007058604.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs10067856",
"effect": "intron_variant",
"frequency_reference_population": 0.098705396,
"gene_hgnc_id": 6824,
"gene_symbol": "MAN2A1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 15020,
"gnomad_genomes_af": 0.0987054,
"gnomad_genomes_homalt": 1025,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1025,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.178,
"pos": 109712432,
"ref": "C",
"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_002372.4"
}
]
}