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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: 19-12657482-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12657482&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 12657482,
"ref": "G",
"alt": "C",
"effect": "stop_gained",
"transcript": "ENST00000456935.7",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.1383C>G",
"hgvs_p": "p.Tyr461*",
"transcript": "NM_000528.4",
"protein_id": "NP_000519.2",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 1011,
"cds_start": 1383,
"cds_end": null,
"cds_length": 3036,
"cdna_start": 1424,
"cdna_end": null,
"cdna_length": 3185,
"mane_select": "ENST00000456935.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.1383C>G",
"hgvs_p": "p.Tyr461*",
"transcript": "ENST00000456935.7",
"protein_id": "ENSP00000395473.2",
"transcript_support_level": 1,
"aa_start": 461,
"aa_end": null,
"aa_length": 1011,
"cds_start": 1383,
"cds_end": null,
"cds_length": 3036,
"cdna_start": 1424,
"cdna_end": null,
"cdna_length": 3185,
"mane_select": "NM_000528.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.1380C>G",
"hgvs_p": "p.Tyr460*",
"transcript": "ENST00000221363.9",
"protein_id": "ENSP00000221363.4",
"transcript_support_level": 1,
"aa_start": 460,
"aa_end": null,
"aa_length": 1010,
"cds_start": 1380,
"cds_end": null,
"cds_length": 3033,
"cdna_start": 1413,
"cdna_end": null,
"cdna_length": 5855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.1386C>G",
"hgvs_p": "p.Tyr462*",
"transcript": "NM_001440570.1",
"protein_id": "NP_001427499.1",
"transcript_support_level": null,
"aa_start": 462,
"aa_end": null,
"aa_length": 1012,
"cds_start": 1386,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 1427,
"cdna_end": null,
"cdna_length": 3188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.1380C>G",
"hgvs_p": "p.Tyr460*",
"transcript": "NM_001173498.2",
"protein_id": "NP_001166969.1",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 1010,
"cds_start": 1380,
"cds_end": null,
"cds_length": 3033,
"cdna_start": 1421,
"cdna_end": null,
"cdna_length": 3182,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "c.282C>G",
"hgvs_p": "p.Tyr94*",
"transcript": "XM_047438841.1",
"protein_id": "XP_047294797.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 644,
"cds_start": 282,
"cds_end": null,
"cds_length": 1935,
"cdna_start": 387,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "n.547C>G",
"hgvs_p": null,
"transcript": "ENST00000465830.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 574,
"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": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "n.1282C>G",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "n.559C>G",
"hgvs_p": null,
"transcript": "ENST00000495617.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "n.-247C>G",
"hgvs_p": null,
"transcript": "ENST00000433513.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "n.-10C>G",
"hgvs_p": null,
"transcript": "ENST00000593686.1",
"protein_id": "ENSP00000471685.1",
"transcript_support_level": 4,
"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": 537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"hgvs_c": "n.-103C>G",
"hgvs_p": null,
"transcript": "ENST00000595880.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MAN2B1",
"gene_hgnc_id": 6826,
"dbsnp": "rs775200333",
"frequency_reference_population": 7.069356e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.06936e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4399999976158142,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": -0.928,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000456935.7",
"gene_symbol": "MAN2B1",
"hgnc_id": 6826,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1383C>G",
"hgvs_p": "p.Tyr461*"
}
],
"clinvar_disease": "Deficiency of alpha-mannosidase,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4",
"phenotype_combined": "Deficiency of alpha-mannosidase|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}