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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: 5-122075443-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=122075443&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 122075443,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002317.7",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.839G>T",
"hgvs_p": "p.Ser280Ile",
"transcript": "NM_002317.7",
"protein_id": "NP_002308.2",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 417,
"cds_start": 839,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000231004.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002317.7"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.839G>T",
"hgvs_p": "p.Ser280Ile",
"transcript": "ENST00000231004.5",
"protein_id": "ENSP00000231004.4",
"transcript_support_level": 1,
"aa_start": 280,
"aa_end": null,
"aa_length": 417,
"cds_start": 839,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002317.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000231004.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.-53G>T",
"hgvs_p": null,
"transcript": "ENST00000513319.5",
"protein_id": "ENSP00000503104.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 120,
"cds_start": null,
"cds_end": null,
"cds_length": 363,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513319.5"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.839G>T",
"hgvs_p": "p.Ser280Ile",
"transcript": "ENST00000939087.1",
"protein_id": "ENSP00000609146.1",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 417,
"cds_start": 839,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000939087.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Ser50Ile",
"transcript": "NM_001178102.2",
"protein_id": "NP_001171573.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 187,
"cds_start": 149,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001178102.2"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Ser50Ile",
"transcript": "ENST00000503759.5",
"protein_id": "ENSP00000503423.1",
"transcript_support_level": 2,
"aa_start": 50,
"aa_end": null,
"aa_length": 187,
"cds_start": 149,
"cds_end": null,
"cds_length": 564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503759.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "c.-53G>T",
"hgvs_p": null,
"transcript": "NM_001317073.1",
"protein_id": "NP_001304002.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 120,
"cds_start": null,
"cds_end": null,
"cds_length": 363,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001317073.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRFBP1",
"gene_hgnc_id": 26333,
"hgvs_c": "c.*118C>A",
"hgvs_p": null,
"transcript": "XM_017009111.3",
"protein_id": "XP_016864600.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": null,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009111.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRFBP1",
"gene_hgnc_id": 26333,
"hgvs_c": "n.440C>A",
"hgvs_p": null,
"transcript": "ENST00000504881.1",
"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": "ENST00000504881.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "n.165G>T",
"hgvs_p": null,
"transcript": "ENST00000505593.5",
"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": "pseudogene",
"feature": "ENST00000505593.5"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "n.*31G>T",
"hgvs_p": null,
"transcript": "ENST00000508067.1",
"protein_id": "ENSP00000427538.1",
"transcript_support_level": 4,
"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": "ENST00000508067.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "n.*31G>T",
"hgvs_p": null,
"transcript": "ENST00000639739.2",
"protein_id": "ENSP00000492324.2",
"transcript_support_level": 5,
"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": "ENST00000639739.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "n.*31G>T",
"hgvs_p": null,
"transcript": "ENST00000508067.1",
"protein_id": "ENSP00000427538.1",
"transcript_support_level": 4,
"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": "ENST00000508067.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"hgvs_c": "n.*31G>T",
"hgvs_p": null,
"transcript": "ENST00000639739.2",
"protein_id": "ENSP00000492324.2",
"transcript_support_level": 5,
"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": "ENST00000639739.2"
}
],
"gene_symbol": "LOX",
"gene_hgnc_id": 6664,
"dbsnp": "rs886040965",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3049927055835724,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.054,
"revel_prediction": "Benign",
"alphamissense_score": 0.4474,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.994,
"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,PP5,BP4",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002317.7",
"gene_symbol": "LOX",
"hgnc_id": 6664,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.839G>T",
"hgvs_p": "p.Ser280Ile"
},
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000504881.1",
"gene_symbol": "SRFBP1",
"hgnc_id": 26333,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.440C>A",
"hgvs_p": null
}
],
"clinvar_disease": " familial thoracic 10,Acute aortic dissection,Aortic aneurysm,Congenital aneurysm of ascending aorta",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Aortic aneurysm, familial thoracic 10|Acute aortic dissection;Congenital aneurysm of ascending aorta",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}