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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: 5-134607010-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=134607010&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 134607010,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000402673.7",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.537T>A",
"hgvs_p": "p.Ser179Arg",
"transcript": "NM_016103.4",
"protein_id": "NP_057187.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 198,
"cds_start": 537,
"cds_end": null,
"cds_length": 597,
"cdna_start": 656,
"cdna_end": null,
"cdna_length": 6517,
"mane_select": "ENST00000402673.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.537T>A",
"hgvs_p": "p.Ser179Arg",
"transcript": "ENST00000402673.7",
"protein_id": "ENSP00000385432.2",
"transcript_support_level": 1,
"aa_start": 179,
"aa_end": null,
"aa_length": 198,
"cds_start": 537,
"cds_end": null,
"cds_length": 597,
"cdna_start": 656,
"cdna_end": null,
"cdna_length": 6517,
"mane_select": "NM_016103.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.537T>A",
"hgvs_p": "p.Ser179Arg",
"transcript": "ENST00000439578.5",
"protein_id": "ENSP00000404997.1",
"transcript_support_level": 1,
"aa_start": 179,
"aa_end": null,
"aa_length": 198,
"cds_start": 537,
"cds_end": null,
"cds_length": 597,
"cdna_start": 721,
"cdna_end": null,
"cdna_length": 929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.333T>A",
"hgvs_p": "p.Ser111Arg",
"transcript": "ENST00000507419.5",
"protein_id": "ENSP00000425339.1",
"transcript_support_level": 1,
"aa_start": 111,
"aa_end": null,
"aa_length": 130,
"cds_start": 333,
"cds_end": null,
"cds_length": 393,
"cdna_start": 1706,
"cdna_end": null,
"cdna_length": 2287,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.537T>A",
"hgvs_p": "p.Ser179Arg",
"transcript": "NM_001033503.3",
"protein_id": "NP_001028675.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 198,
"cds_start": 537,
"cds_end": null,
"cds_length": 597,
"cdna_start": 775,
"cdna_end": null,
"cdna_length": 6636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.333T>A",
"hgvs_p": "p.Ser111Arg",
"transcript": "ENST00000502539.5",
"protein_id": "ENSP00000426335.1",
"transcript_support_level": 5,
"aa_start": 111,
"aa_end": null,
"aa_length": 130,
"cds_start": 333,
"cds_end": null,
"cds_length": 393,
"cdna_start": 436,
"cdna_end": null,
"cdna_length": 708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.333T>A",
"hgvs_p": "p.Ser111Arg",
"transcript": "ENST00000509937.5",
"protein_id": "ENSP00000424673.1",
"transcript_support_level": 5,
"aa_start": 111,
"aa_end": null,
"aa_length": 130,
"cds_start": 333,
"cds_end": null,
"cds_length": 393,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.333T>A",
"hgvs_p": "p.Ser111Arg",
"transcript": "ENST00000509730.5",
"protein_id": "ENSP00000423197.1",
"transcript_support_level": 2,
"aa_start": 111,
"aa_end": null,
"aa_length": 117,
"cds_start": 333,
"cds_end": null,
"cds_length": 356,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.537T>A",
"hgvs_p": "p.Ser179Arg",
"transcript": "XM_047417257.1",
"protein_id": "XP_047273213.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 198,
"cds_start": 537,
"cds_end": null,
"cds_length": 597,
"cdna_start": 678,
"cdna_end": null,
"cdna_length": 6539,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.333T>A",
"hgvs_p": "p.Ser111Arg",
"transcript": "XM_047417258.1",
"protein_id": "XP_047273214.1",
"transcript_support_level": null,
"aa_start": 111,
"aa_end": null,
"aa_length": 130,
"cds_start": 333,
"cds_end": null,
"cds_length": 393,
"cdna_start": 378,
"cdna_end": null,
"cdna_length": 6239,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "n.*260T>A",
"hgvs_p": null,
"transcript": "ENST00000503318.5",
"protein_id": "ENSP00000425367.1",
"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": 733,
"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": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "n.2506T>A",
"hgvs_p": null,
"transcript": "ENST00000508363.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 3086,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "n.*260T>A",
"hgvs_p": null,
"transcript": "ENST00000503318.5",
"protein_id": "ENSP00000425367.1",
"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": 733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"hgvs_c": "c.*27T>A",
"hgvs_p": null,
"transcript": "ENST00000505758.5",
"protein_id": "ENSP00000425466.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": -4,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SAR1B",
"gene_hgnc_id": 10535,
"dbsnp": "rs28942110",
"frequency_reference_population": 0.000035315286,
"hom_count_reference_population": 0,
"allele_count_reference_population": 57,
"gnomad_exomes_af": 0.0000383084,
"gnomad_genomes_af": 0.00000656978,
"gnomad_exomes_ac": 56,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9809232950210571,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.89,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9994,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.37,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.118,
"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": "Likely_pathogenic",
"acmg_criteria": "PM2,PP2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM2",
"PP2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000402673.7",
"gene_symbol": "SAR1B",
"hgnc_id": 10535,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.537T>A",
"hgvs_p": "p.Ser179Arg"
}
],
"clinvar_disease": "Chylomicron retention disease,SAR1B-related disorder",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1 O:1",
"phenotype_combined": "Chylomicron retention disease|SAR1B-related disorder",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}