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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: 1-63415881-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=63415881&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 63415881,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000263440.6",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "c.911C>T",
"hgvs_p": "p.Ser304Phe",
"transcript": "NM_013339.4",
"protein_id": "NP_037471.2",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 507,
"cds_start": 911,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1179,
"cdna_end": null,
"cdna_length": 3325,
"mane_select": "ENST00000263440.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "c.911C>T",
"hgvs_p": "p.Ser304Phe",
"transcript": "ENST00000263440.6",
"protein_id": "ENSP00000263440.5",
"transcript_support_level": 5,
"aa_start": 304,
"aa_end": null,
"aa_length": 507,
"cds_start": 911,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1179,
"cdna_end": null,
"cdna_length": 3325,
"mane_select": "NM_013339.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.500C>T",
"hgvs_p": null,
"transcript": "ENST00000465969.5",
"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": 915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*60C>T",
"hgvs_p": null,
"transcript": "ENST00000603108.6",
"protein_id": "ENSP00000473934.2",
"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": 2055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*217C>T",
"hgvs_p": null,
"transcript": "ENST00000647818.1",
"protein_id": "ENSP00000497667.1",
"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": 1841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*640C>T",
"hgvs_p": null,
"transcript": "ENST00000648964.1",
"protein_id": "ENSP00000497828.1",
"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": 1887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*333C>T",
"hgvs_p": null,
"transcript": "ENST00000649570.1",
"protein_id": "ENSP00000497742.1",
"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": 2047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*268C>T",
"hgvs_p": null,
"transcript": "ENST00000650494.1",
"protein_id": "ENSP00000497170.1",
"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": 1422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*60C>T",
"hgvs_p": null,
"transcript": "ENST00000603108.6",
"protein_id": "ENSP00000473934.2",
"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": 2055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*217C>T",
"hgvs_p": null,
"transcript": "ENST00000647818.1",
"protein_id": "ENSP00000497667.1",
"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": 1841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*640C>T",
"hgvs_p": null,
"transcript": "ENST00000648964.1",
"protein_id": "ENSP00000497828.1",
"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": 1887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*333C>T",
"hgvs_p": null,
"transcript": "ENST00000649570.1",
"protein_id": "ENSP00000497742.1",
"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": 2047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"hgvs_c": "n.*268C>T",
"hgvs_p": null,
"transcript": "ENST00000650494.1",
"protein_id": "ENSP00000497170.1",
"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": 1422,
"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": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ITGB3BP",
"gene_hgnc_id": 6157,
"hgvs_c": "n.339+38037G>A",
"hgvs_p": null,
"transcript": "ENST00000717656.1",
"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": 743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALG6",
"gene_hgnc_id": 23157,
"dbsnp": "rs4630153",
"frequency_reference_population": 0.7177138,
"hom_count_reference_population": 416603,
"allele_count_reference_population": 1149644,
"gnomad_exomes_af": 0.713547,
"gnomad_genomes_af": 0.757437,
"gnomad_exomes_ac": 1034456,
"gnomad_genomes_ac": 115188,
"gnomad_exomes_homalt": 372394,
"gnomad_genomes_homalt": 44209,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000016998650380628533,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.25,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.187,
"revel_prediction": "Benign",
"alphamissense_score": 0.0439,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.653,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.25,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000263440.6",
"gene_symbol": "ALG6",
"hgnc_id": 23157,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.911C>T",
"hgvs_p": "p.Ser304Phe"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000717656.1",
"gene_symbol": "ITGB3BP",
"hgnc_id": 6157,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.339+38037G>A",
"hgvs_p": null
}
],
"clinvar_disease": "ALG6-congenital disorder of glycosylation 1C,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:6",
"phenotype_combined": "not specified|ALG6-congenital disorder of glycosylation 1C|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}