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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: 18-79973765-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=79973765&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 79973765,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_006701.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.349G>T",
"hgvs_p": "p.Glu117*",
"transcript": "NM_006701.5",
"protein_id": "NP_006692.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 142,
"cds_start": 349,
"cds_end": null,
"cds_length": 429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000269601.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006701.5"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.349G>T",
"hgvs_p": "p.Glu117*",
"transcript": "ENST00000269601.10",
"protein_id": "ENSP00000269601.4",
"transcript_support_level": 1,
"aa_start": 117,
"aa_end": null,
"aa_length": 142,
"cds_start": 349,
"cds_end": null,
"cds_length": 429,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006701.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000269601.10"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.136G>T",
"hgvs_p": "p.Glu46*",
"transcript": "ENST00000585474.5",
"protein_id": "ENSP00000465572.1",
"transcript_support_level": 1,
"aa_start": 46,
"aa_end": null,
"aa_length": 71,
"cds_start": 136,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000585474.5"
},
{
"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": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "n.*143G>T",
"hgvs_p": null,
"transcript": "ENST00000355491.5",
"protein_id": "ENSP00000347678.4",
"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": "nonsense_mediated_decay",
"feature": "ENST00000355491.5"
},
{
"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": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "n.*143G>T",
"hgvs_p": null,
"transcript": "ENST00000355491.5",
"protein_id": "ENSP00000347678.4",
"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": "nonsense_mediated_decay",
"feature": "ENST00000355491.5"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.325G>T",
"hgvs_p": "p.Glu109*",
"transcript": "NM_001305557.2",
"protein_id": "NP_001292486.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 134,
"cds_start": 325,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001305557.2"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.232G>T",
"hgvs_p": "p.Glu78*",
"transcript": "NM_001303471.3",
"protein_id": "NP_001290400.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 103,
"cds_start": 232,
"cds_end": null,
"cds_length": 312,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303471.3"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.136G>T",
"hgvs_p": "p.Glu46*",
"transcript": "NM_001305563.2",
"protein_id": "NP_001292492.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 71,
"cds_start": 136,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001305563.2"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.136G>T",
"hgvs_p": "p.Glu46*",
"transcript": "NM_001305564.2",
"protein_id": "NP_001292493.1",
"transcript_support_level": null,
"aa_start": 46,
"aa_end": null,
"aa_length": 71,
"cds_start": 136,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001305564.2"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.136G>T",
"hgvs_p": "p.Glu46*",
"transcript": "ENST00000592837.1",
"protein_id": "ENSP00000468761.1",
"transcript_support_level": 2,
"aa_start": 46,
"aa_end": null,
"aa_length": 71,
"cds_start": 136,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000592837.1"
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.136G>T",
"hgvs_p": "p.Glu46*",
"transcript": "ENST00000592957.1",
"protein_id": "ENSP00000465493.1",
"transcript_support_level": 3,
"aa_start": 46,
"aa_end": null,
"aa_length": 71,
"cds_start": 136,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000592957.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "c.*71G>T",
"hgvs_p": null,
"transcript": "ENST00000588162.1",
"protein_id": "ENSP00000465321.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 57,
"cds_start": null,
"cds_end": null,
"cds_length": 174,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000588162.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "n.*403G>T",
"hgvs_p": null,
"transcript": "ENST00000585769.5",
"protein_id": "ENSP00000466266.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000585769.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "n.225G>T",
"hgvs_p": null,
"transcript": "ENST00000586612.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000586612.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "n.739G>T",
"hgvs_p": null,
"transcript": "NR_131175.2",
"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": "NR_131175.2"
},
{
"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": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "n.590G>T",
"hgvs_p": null,
"transcript": "NR_131176.2",
"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": "NR_131176.2"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "n.416G>T",
"hgvs_p": null,
"transcript": "NR_131177.2",
"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": "NR_131177.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"hgvs_c": "n.*403G>T",
"hgvs_p": null,
"transcript": "ENST00000585769.5",
"protein_id": "ENSP00000466266.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000585769.5"
}
],
"gene_symbol": "TXNL4A",
"gene_hgnc_id": 30551,
"dbsnp": "rs727502793",
"frequency_reference_population": 0.0000027361764,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273618,
"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": 0.6499999761581421,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.65,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.732,
"phylop100way_prediction": "Uncertain_significance",
"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": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_006701.5",
"gene_symbol": "TXNL4A",
"hgnc_id": 30551,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.349G>T",
"hgvs_p": "p.Glu117*"
}
],
"clinvar_disease": "Choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome,TXNL4A-related disorder",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1 O:1",
"phenotype_combined": "Choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome|TXNL4A-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}