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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: X-149500991-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=149500991&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 149500991,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000340855.11",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "c.465T>A",
"hgvs_p": "p.Phe155Leu",
"transcript": "NM_000202.8",
"protein_id": "NP_000193.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 550,
"cds_start": 465,
"cds_end": null,
"cds_length": 1653,
"cdna_start": 634,
"cdna_end": null,
"cdna_length": 7580,
"mane_select": "ENST00000340855.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "c.465T>A",
"hgvs_p": "p.Phe155Leu",
"transcript": "ENST00000340855.11",
"protein_id": "ENSP00000339801.6",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 550,
"cds_start": 465,
"cds_end": null,
"cds_length": 1653,
"cdna_start": 634,
"cdna_end": null,
"cdna_length": 7580,
"mane_select": "NM_000202.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "c.465T>A",
"hgvs_p": "p.Phe155Leu",
"transcript": "ENST00000370441.8",
"protein_id": "ENSP00000359470.4",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 343,
"cds_start": 465,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 675,
"cdna_end": null,
"cdna_length": 1399,
"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": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "n.465T>A",
"hgvs_p": null,
"transcript": "ENST00000466323.5",
"protein_id": "ENSP00000418264.1",
"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": 1529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000241489",
"gene_hgnc_id": null,
"hgvs_c": "c.-169T>A",
"hgvs_p": null,
"transcript": "ENST00000651111.1",
"protein_id": "ENSP00000498395.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 339,
"cds_start": -4,
"cds_end": null,
"cds_length": 1020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "c.195T>A",
"hgvs_p": "p.Phe65Leu",
"transcript": "NM_001166550.4",
"protein_id": "NP_001160022.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 460,
"cds_start": 195,
"cds_end": null,
"cds_length": 1383,
"cdna_start": 590,
"cdna_end": null,
"cdna_length": 7536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "c.465T>A",
"hgvs_p": "p.Phe155Leu",
"transcript": "NM_006123.5",
"protein_id": "NP_006114.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 343,
"cds_start": 465,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 634,
"cdna_end": null,
"cdna_length": 1358,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "n.*70T>A",
"hgvs_p": null,
"transcript": "ENST00000464251.5",
"protein_id": "ENSP00000428980.1",
"transcript_support_level": 5,
"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": 959,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "n.124T>A",
"hgvs_p": null,
"transcript": "ENST00000490775.5",
"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": 945,
"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": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "n.634T>A",
"hgvs_p": null,
"transcript": "NR_104128.2",
"protein_id": null,
"transcript_support_level": null,
"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": 1488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000241489",
"gene_hgnc_id": null,
"hgvs_c": "c.-169T>A",
"hgvs_p": null,
"transcript": "ENST00000422081.6",
"protein_id": "ENSP00000477056.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 339,
"cds_start": -4,
"cds_end": null,
"cds_length": 1020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"hgvs_c": "n.*70T>A",
"hgvs_p": null,
"transcript": "ENST00000464251.5",
"protein_id": "ENSP00000428980.1",
"transcript_support_level": 5,
"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": 959,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000241489",
"gene_hgnc_id": null,
"hgvs_c": "n.114-13893T>A",
"hgvs_p": null,
"transcript": "ENST00000441880.1",
"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": 416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IDS",
"gene_hgnc_id": 5389,
"dbsnp": "rs149210251",
"frequency_reference_population": 0.0013441087,
"hom_count_reference_population": 439,
"allele_count_reference_population": 1591,
"gnomad_exomes_af": 0.000693014,
"gnomad_genomes_af": 0.00760163,
"gnomad_exomes_ac": 743,
"gnomad_genomes_ac": 848,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 8,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0029900074005126953,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.329,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1967,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.117,
"phylop100way_prediction": "Benign",
"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": "Benign",
"acmg_criteria": "PS1,PM1,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 20,
"pathogenic_score": 6,
"criteria": [
"PS1",
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000340855.11",
"gene_symbol": "IDS",
"hgnc_id": 5389,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.465T>A",
"hgvs_p": "p.Phe155Leu"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000651111.1",
"gene_symbol": "ENSG00000241489",
"hgnc_id": null,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.-169T>A",
"hgvs_p": null
}
],
"clinvar_disease": " MPS-II, MPS-III-A,IDS-related disorder,Inborn genetic diseases,Mucopolysaccharidosis,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not provided|Mucopolysaccharidosis, MPS-II|Mucopolysaccharidosis, MPS-III-A|Inborn genetic diseases|IDS-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}