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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: 9-98836982-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=98836982&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 98836982,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_024642.5",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.1046G>A",
"hgvs_p": "p.Cys349Tyr",
"transcript": "NM_024642.5",
"protein_id": "NP_078918.3",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 581,
"cds_start": 1046,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 1075,
"cdna_end": null,
"cdna_length": 2764,
"mane_select": "ENST00000375011.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024642.5"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.1046G>A",
"hgvs_p": "p.Cys349Tyr",
"transcript": "ENST00000375011.4",
"protein_id": "ENSP00000364150.3",
"transcript_support_level": 1,
"aa_start": 349,
"aa_end": null,
"aa_length": 581,
"cds_start": 1046,
"cds_end": null,
"cds_length": 1746,
"cdna_start": 1075,
"cdna_end": null,
"cdna_length": 2764,
"mane_select": "NM_024642.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375011.4"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.1166G>A",
"hgvs_p": "p.Cys389Tyr",
"transcript": "ENST00000969913.1",
"protein_id": "ENSP00000639972.1",
"transcript_support_level": null,
"aa_start": 389,
"aa_end": null,
"aa_length": 621,
"cds_start": 1166,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 1194,
"cdna_end": null,
"cdna_length": 2879,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969913.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.1046G>A",
"hgvs_p": "p.Cys349Tyr",
"transcript": "ENST00000969912.1",
"protein_id": "ENSP00000639971.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 596,
"cds_start": 1046,
"cds_end": null,
"cds_length": 1791,
"cdna_start": 1073,
"cdna_end": null,
"cdna_length": 2805,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969912.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.1046G>A",
"hgvs_p": "p.Cys349Tyr",
"transcript": "ENST00000931580.1",
"protein_id": "ENSP00000601639.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 579,
"cds_start": 1046,
"cds_end": null,
"cds_length": 1740,
"cdna_start": 1074,
"cdna_end": null,
"cdna_length": 2754,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931580.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.959G>A",
"hgvs_p": "p.Cys320Tyr",
"transcript": "ENST00000931577.1",
"protein_id": "ENSP00000601636.1",
"transcript_support_level": null,
"aa_start": 320,
"aa_end": null,
"aa_length": 552,
"cds_start": 959,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 1045,
"cdna_end": null,
"cdna_length": 3919,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931577.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.1046G>A",
"hgvs_p": "p.Cys349Tyr",
"transcript": "ENST00000931578.1",
"protein_id": "ENSP00000601637.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 532,
"cds_start": 1046,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 1107,
"cdna_end": null,
"cdna_length": 2649,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931578.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.860G>A",
"hgvs_p": "p.Cys287Tyr",
"transcript": "ENST00000931579.1",
"protein_id": "ENSP00000601638.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 519,
"cds_start": 860,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 921,
"cdna_end": null,
"cdna_length": 2608,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931579.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.824G>A",
"hgvs_p": "p.Cys275Tyr",
"transcript": "XM_011519018.3",
"protein_id": "XP_011517320.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 507,
"cds_start": 824,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1719,
"cdna_end": null,
"cdna_length": 3408,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011519018.3"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.794G>A",
"hgvs_p": "p.Cys265Tyr",
"transcript": "XM_017015133.1",
"protein_id": "XP_016870622.1",
"transcript_support_level": null,
"aa_start": 265,
"aa_end": null,
"aa_length": 497,
"cds_start": 794,
"cds_end": null,
"cds_length": 1494,
"cdna_start": 806,
"cdna_end": null,
"cdna_length": 2495,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017015133.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.338G>A",
"hgvs_p": "p.Cys113Tyr",
"transcript": "XM_011519020.2",
"protein_id": "XP_011517322.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 345,
"cds_start": 338,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 428,
"cdna_end": null,
"cdna_length": 2117,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011519020.2"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.155G>A",
"hgvs_p": "p.Cys52Tyr",
"transcript": "XM_006717287.1",
"protein_id": "XP_006717350.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 284,
"cds_start": 155,
"cds_end": null,
"cds_length": 855,
"cdna_start": 862,
"cdna_end": null,
"cdna_length": 2551,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006717287.1"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "c.155G>A",
"hgvs_p": "p.Cys52Tyr",
"transcript": "XM_047423871.1",
"protein_id": "XP_047279827.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 284,
"cds_start": 155,
"cds_end": null,
"cds_length": 855,
"cdna_start": 692,
"cdna_end": null,
"cdna_length": 2381,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423871.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"hgvs_c": "n.-93G>A",
"hgvs_p": null,
"transcript": "ENST00000615204.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 633,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000615204.1"
}
],
"gene_symbol": "GALNT12",
"gene_hgnc_id": 19877,
"dbsnp": "rs747921962",
"frequency_reference_population": 0.0000024783546,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.0000013681,
"gnomad_genomes_af": 0.0000131498,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9559487104415894,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.761,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9959,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_024642.5",
"gene_symbol": "GALNT12",
"hgnc_id": 19877,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.1046G>A",
"hgvs_p": "p.Cys349Tyr"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}