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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: 2-43675952-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=43675952&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 43675952,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001101330.3",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1GALT1C1L",
"gene_hgnc_id": 51617,
"hgvs_c": "c.371A>C",
"hgvs_p": "p.Tyr124Ser",
"transcript": "NM_001101330.3",
"protein_id": "NP_001094800.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 315,
"cds_start": 371,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000475092.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001101330.3"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "C1GALT1C1L",
"gene_hgnc_id": 51617,
"hgvs_c": "c.371A>C",
"hgvs_p": "p.Tyr124Ser",
"transcript": "ENST00000475092.4",
"protein_id": "ENSP00000489061.1",
"transcript_support_level": 6,
"aa_start": 124,
"aa_end": null,
"aa_length": 315,
"cds_start": 371,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001101330.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000475092.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "NM_172069.4",
"protein_id": "NP_742066.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1493,
"cds_start": null,
"cds_end": null,
"cds_length": 4482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000282406.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172069.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "ENST00000282406.9",
"protein_id": "ENSP00000282406.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1493,
"cds_start": null,
"cds_end": null,
"cds_length": 4482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_172069.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000282406.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "n.401-2911T>G",
"hgvs_p": null,
"transcript": "ENST00000405000.6",
"protein_id": null,
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000405000.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "ENST00000923731.1",
"protein_id": "ENSP00000593790.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1493,
"cds_start": null,
"cds_end": null,
"cds_length": 4482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923731.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "ENST00000958645.1",
"protein_id": "ENSP00000628704.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1492,
"cds_start": null,
"cds_end": null,
"cds_length": 4479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958645.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "ENST00000890790.1",
"protein_id": "ENSP00000560849.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1488,
"cds_start": null,
"cds_end": null,
"cds_length": 4467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890790.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.1-2911T>G",
"hgvs_p": null,
"transcript": "XM_017003351.3",
"protein_id": "XP_016858840.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1452,
"cds_start": null,
"cds_end": null,
"cds_length": 4359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003351.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "XM_047443340.1",
"protein_id": "XP_047299296.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1099,
"cds_start": null,
"cds_end": null,
"cds_length": 3300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443340.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "XM_047443341.1",
"protein_id": "XP_047299297.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1062,
"cds_start": null,
"cds_end": null,
"cds_length": 3189,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443341.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "XM_017003352.2",
"protein_id": "XP_016858841.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1013,
"cds_start": null,
"cds_end": null,
"cds_length": 3042,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003352.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null,
"transcript": "XM_047443343.1",
"protein_id": "XP_047299299.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 896,
"cds_start": null,
"cds_end": null,
"cds_length": 2691,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443343.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "n.207-2911T>G",
"hgvs_p": null,
"transcript": "ENST00000405223.6",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000405223.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "n.124-2911T>G",
"hgvs_p": null,
"transcript": "ENST00000491692.5",
"protein_id": "ENSP00000427746.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000491692.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "n.247-2911T>G",
"hgvs_p": null,
"transcript": "XR_001738620.2",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001738620.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLEKHH2",
"gene_hgnc_id": 30506,
"hgvs_c": "n.247-2911T>G",
"hgvs_p": null,
"transcript": "XR_001738621.2",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001738621.2"
}
],
"gene_symbol": "C1GALT1C1L",
"gene_hgnc_id": 51617,
"dbsnp": "rs1558461776",
"frequency_reference_population": 0.0000027365322,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273653,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7304449081420898,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.3006,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.553,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001101330.3",
"gene_symbol": "C1GALT1C1L",
"hgnc_id": 51617,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.371A>C",
"hgvs_p": "p.Tyr124Ser"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_172069.4",
"gene_symbol": "PLEKHH2",
"hgnc_id": 30506,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.124-2911T>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}