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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: 5-74720644-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=74720644&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "HEXB",
"hgnc_id": 4879,
"hgvs_c": "c.1510C>G",
"hgvs_p": "p.Pro504Ala",
"inheritance_mode": "AR",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_000521.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3",
"acmg_score": 7,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.8574,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.58,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9864604473114014,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 556,
"aa_ref": "P",
"aa_start": 504,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1812,
"cdna_start": 1538,
"cds_end": null,
"cds_length": 1671,
"cds_start": 1510,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_000521.4",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "c.1510C>G",
"hgvs_p": "p.Pro504Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000261416.12",
"protein_coding": true,
"protein_id": "NP_000512.2",
"strand": true,
"transcript": "NM_000521.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 556,
"aa_ref": "P",
"aa_start": 504,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1812,
"cdna_start": 1538,
"cds_end": null,
"cds_length": 1671,
"cds_start": 1510,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000261416.12",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "c.1510C>G",
"hgvs_p": "p.Pro504Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000521.4",
"protein_coding": true,
"protein_id": "ENSP00000261416.7",
"strand": true,
"transcript": "ENST00000261416.12",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 331,
"aa_ref": "P",
"aa_start": 279,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2021,
"cdna_start": 1747,
"cds_end": null,
"cds_length": 996,
"cds_start": 835,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000511181.5",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "c.835C>G",
"hgvs_p": "p.Pro279Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000426285.1",
"strand": true,
"transcript": "ENST00000511181.5",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 331,
"aa_ref": "P",
"aa_start": 279,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2021,
"cdna_start": 1747,
"cds_end": null,
"cds_length": 996,
"cds_start": 835,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001292004.2",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "c.835C>G",
"hgvs_p": "p.Pro279Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278933.1",
"strand": true,
"transcript": "NM_001292004.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 201,
"aa_ref": "P",
"aa_start": 149,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 720,
"cdna_start": 446,
"cds_end": null,
"cds_length": 606,
"cds_start": 445,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000513336.5",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "c.445C>G",
"hgvs_p": "p.Pro149Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423713.1",
"strand": true,
"transcript": "ENST00000513336.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 35,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 806,
"cdna_start": null,
"cds_end": null,
"cds_length": 108,
"cds_start": null,
"consequences": [
"splice_region_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000509579.1",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "c.-54C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424939.1",
"strand": true,
"transcript": "ENST00000509579.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 35,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 806,
"cdna_start": null,
"cds_end": null,
"cds_length": 108,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000509579.1",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "c.-54C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424939.1",
"strand": true,
"transcript": "ENST00000509579.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 756,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000503312.5",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "n.385C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000426384.1",
"strand": true,
"transcript": "ENST00000503312.5",
"transcript_support_level": 5
},
{
"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": 899,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000504459.5",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "n.707C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000504459.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 604,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000505859.1",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "n.31C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000424550.1",
"strand": true,
"transcript": "ENST00000505859.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 502,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000513539.1",
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"hgvs_c": "n.229C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000513539.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.995618830681449,
"dbsnp": "rs121907985",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": 6.8421264e-7,
"gene_hgnc_id": 4879,
"gene_symbol": "HEXB",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84213e-7,
"gnomad_exomes_homalt": 0,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.715,
"pos": 74720644,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.943,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9539999961853027,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000521.4"
}
]
}