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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-48904799-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=48904799&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 48904799,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_005660.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.520A>G",
"hgvs_p": "p.Thr174Ala",
"transcript": "ENST00000445167.7",
"protein_id": "ENSP00000402726.2",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 242,
"cds_start": 520,
"cds_end": null,
"cds_length": 729,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 1739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.1110A>G",
"hgvs_p": "p.Pro370Pro",
"transcript": "NM_005660.3",
"protein_id": "NP_005651.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 396,
"cds_start": 1110,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1120,
"cdna_end": null,
"cdna_length": 1456,
"mane_select": "ENST00000247138.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.1110A>G",
"hgvs_p": "p.Pro370Pro",
"transcript": "ENST00000247138.11",
"protein_id": "ENSP00000247138.5",
"transcript_support_level": 1,
"aa_start": 370,
"aa_end": null,
"aa_length": 396,
"cds_start": 1110,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1120,
"cdna_end": null,
"cdna_length": 1456,
"mane_select": "NM_005660.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.1110A>G",
"hgvs_p": "p.Pro370Pro",
"transcript": "ENST00000376521.6",
"protein_id": "ENSP00000365704.1",
"transcript_support_level": 1,
"aa_start": 370,
"aa_end": null,
"aa_length": 393,
"cds_start": 1110,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 3047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.520A>G",
"hgvs_p": "p.Thr174Ala",
"transcript": "NM_001032289.3",
"protein_id": "NP_001027460.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 242,
"cds_start": 520,
"cds_end": null,
"cds_length": 729,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 1716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.520A>G",
"hgvs_p": "p.Thr174Ala",
"transcript": "NM_001282647.2",
"protein_id": "NP_001269576.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 224,
"cds_start": 520,
"cds_end": null,
"cds_length": 675,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.520A>G",
"hgvs_p": "p.Thr174Ala",
"transcript": "ENST00000376529.8",
"protein_id": "ENSP00000365712.3",
"transcript_support_level": 3,
"aa_start": 174,
"aa_end": null,
"aa_length": 224,
"cds_start": 520,
"cds_end": null,
"cds_length": 675,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.448A>G",
"hgvs_p": "p.Thr150Ala",
"transcript": "NM_001282648.2",
"protein_id": "NP_001269577.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 218,
"cds_start": 448,
"cds_end": null,
"cds_length": 657,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 1715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.448A>G",
"hgvs_p": "p.Thr150Ala",
"transcript": "ENST00000376515.8",
"protein_id": "ENSP00000365698.3",
"transcript_support_level": 3,
"aa_start": 150,
"aa_end": null,
"aa_length": 218,
"cds_start": 448,
"cds_end": null,
"cds_length": 657,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 1044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.1194A>G",
"hgvs_p": "p.Pro398Pro",
"transcript": "NM_001282651.2",
"protein_id": "NP_001269580.1",
"transcript_support_level": null,
"aa_start": 398,
"aa_end": null,
"aa_length": 421,
"cds_start": 1194,
"cds_end": null,
"cds_length": 1266,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 2820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.1194A>G",
"hgvs_p": "p.Pro398Pro",
"transcript": "ENST00000452555.7",
"protein_id": "ENSP00000416002.2",
"transcript_support_level": 2,
"aa_start": 398,
"aa_end": null,
"aa_length": 421,
"cds_start": 1194,
"cds_end": null,
"cds_length": 1266,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 1563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.1149A>G",
"hgvs_p": "p.Pro383Pro",
"transcript": "NM_001282650.2",
"protein_id": "NP_001269579.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 406,
"cds_start": 1149,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 1159,
"cdna_end": null,
"cdna_length": 2775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.1149A>G",
"hgvs_p": "p.Pro383Pro",
"transcript": "ENST00000616181.5",
"protein_id": "ENSP00000478617.1",
"transcript_support_level": 2,
"aa_start": 383,
"aa_end": null,
"aa_length": 406,
"cds_start": 1149,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 1159,
"cdna_end": null,
"cdna_length": 1614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.1110A>G",
"hgvs_p": "p.Pro370Pro",
"transcript": "NM_001042498.3",
"protein_id": "NP_001035963.1",
"transcript_support_level": null,
"aa_start": 370,
"aa_end": null,
"aa_length": 393,
"cds_start": 1110,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 1120,
"cdna_end": null,
"cdna_length": 2736,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.927A>G",
"hgvs_p": "p.Pro309Pro",
"transcript": "NM_001282649.2",
"protein_id": "NP_001269578.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 332,
"cds_start": 927,
"cds_end": null,
"cds_length": 999,
"cdna_start": 937,
"cdna_end": null,
"cdna_length": 2553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.927A>G",
"hgvs_p": "p.Pro309Pro",
"transcript": "ENST00000635589.1",
"protein_id": "ENSP00000489197.1",
"transcript_support_level": 2,
"aa_start": 309,
"aa_end": null,
"aa_length": 332,
"cds_start": 927,
"cds_end": null,
"cds_length": 999,
"cdna_start": 937,
"cdna_end": null,
"cdna_length": 1424,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "n.1110A>G",
"hgvs_p": null,
"transcript": "ENST00000635285.1",
"protein_id": "ENSP00000489484.1",
"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": 2046,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "n.*1004A>G",
"hgvs_p": null,
"transcript": "ENST00000635628.1",
"protein_id": "ENSP00000489613.1",
"transcript_support_level": 4,
"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": 2812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.*65A>G",
"hgvs_p": null,
"transcript": "ENST00000413561.7",
"protein_id": "ENSP00000393233.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 201,
"cds_start": -4,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1857,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "n.*1004A>G",
"hgvs_p": null,
"transcript": "ENST00000635628.1",
"protein_id": "ENSP00000489613.1",
"transcript_support_level": 4,
"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": 2812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.424-1334A>G",
"hgvs_p": null,
"transcript": "ENST00000635460.1",
"protein_id": "ENSP00000489339.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 174,
"cds_start": -4,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"dbsnp": "rs782273947",
"frequency_reference_population": 0.000014070437,
"hom_count_reference_population": 5,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000145794,
"gnomad_genomes_af": 0.00000902812,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1060841977596283,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.059,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.87,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.405,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005660.3",
"gene_symbol": "SLC35A2",
"hgnc_id": 11022,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,Unknown",
"hgvs_c": "c.1110A>G",
"hgvs_p": "p.Pro370Pro"
}
],
"clinvar_disease": "SLC35A2-congenital disorder of glycosylation",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "SLC35A2-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}