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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: 17-28402276-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=28402276&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PM5",
"PP3_Moderate",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC46A1",
"hgnc_id": 30521,
"hgvs_c": "c.1127G>A",
"hgvs_p": "p.Arg376Gln",
"inheritance_mode": "AR",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_080669.6",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3_Moderate",
"PP5"
],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "SARM1",
"hgnc_id": 17074,
"hgvs_c": "c.*5990C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 9,
"score": 9,
"transcript": "NM_015077.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PM5,PP3_Moderate,PP5",
"acmg_score": 11,
"allele_count_reference_population": 16,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.3175,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.36,
"chr": "17",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Congenital defect of folate absorption,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 US:1 O:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8969739079475403,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 459,
"aa_ref": "R",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6492,
"cdna_start": 1225,
"cds_end": null,
"cds_length": 1380,
"cds_start": 1127,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_080669.6",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.1127G>A",
"hgvs_p": "p.Arg376Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000612814.5",
"protein_coding": true,
"protein_id": "NP_542400.2",
"strand": false,
"transcript": "NM_080669.6",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 459,
"aa_ref": "R",
"aa_start": 376,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6492,
"cdna_start": 1225,
"cds_end": null,
"cds_length": 1380,
"cds_start": 1127,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000612814.5",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.1127G>A",
"hgvs_p": "p.Arg376Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_080669.6",
"protein_coding": true,
"protein_id": "ENSP00000480703.1",
"strand": false,
"transcript": "ENST00000612814.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 724,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10277,
"cdna_start": null,
"cds_end": null,
"cds_length": 2175,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_015077.4",
"gene_hgnc_id": 17074,
"gene_symbol": "SARM1",
"hgvs_c": "c.*5990C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000585482.6",
"protein_coding": true,
"protein_id": "NP_055892.2",
"strand": true,
"transcript": "NM_015077.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 724,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 10277,
"cdna_start": null,
"cds_end": null,
"cds_length": 2175,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000585482.6",
"gene_hgnc_id": 17074,
"gene_symbol": "SARM1",
"hgvs_c": "c.*5990C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015077.4",
"protein_coding": true,
"protein_id": "ENSP00000468032.2",
"strand": true,
"transcript": "ENST00000585482.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 431,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5363,
"cdna_start": null,
"cds_end": null,
"cds_length": 1296,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000618626.1",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.1082-1510G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000483652.1",
"strand": false,
"transcript": "ENST00000618626.1",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 399,
"aa_ref": "R",
"aa_start": 316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1936,
"cdna_start": 1045,
"cds_end": null,
"cds_length": 1200,
"cds_start": 947,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000884019.1",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.947G>A",
"hgvs_p": "p.Arg316Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554078.1",
"strand": false,
"transcript": "ENST00000884019.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 385,
"aa_ref": "R",
"aa_start": 302,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6413,
"cdna_start": 1146,
"cds_end": null,
"cds_length": 1158,
"cds_start": 905,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017024110.2",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.905G>A",
"hgvs_p": "p.Arg302Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016879599.1",
"strand": false,
"transcript": "XM_017024110.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 431,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6408,
"cdna_start": null,
"cds_end": null,
"cds_length": 1296,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001242366.3",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.1082-1510G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001229295.1",
"strand": false,
"transcript": "NM_001242366.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 371,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2138,
"cdna_start": null,
"cds_end": null,
"cds_length": 1116,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000942091.1",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.902-1510G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612150.1",
"strand": false,
"transcript": "ENST00000942091.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 123,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 574,
"cdna_start": null,
"cds_end": null,
"cds_length": 372,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000582735.1",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.205+2340G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000463339.1",
"strand": false,
"transcript": "ENST00000582735.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 415,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6251,
"cdna_start": null,
"cds_end": null,
"cds_length": 1248,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005277786.4",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.1081+2340G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005277843.1",
"strand": false,
"transcript": "XM_005277786.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 357,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6329,
"cdna_start": null,
"cds_end": null,
"cds_length": 1074,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047435279.1",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.860-1510G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047291235.1",
"strand": false,
"transcript": "XM_047435279.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 341,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6172,
"cdna_start": null,
"cds_end": null,
"cds_length": 1026,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047435280.1",
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"hgvs_c": "c.859+2340G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047291236.1",
"strand": false,
"transcript": "XM_047435280.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs281875211",
"effect": "missense_variant",
"frequency_reference_population": 0.000009916515,
"gene_hgnc_id": 30521,
"gene_symbol": "SLC46A1",
"gnomad_exomes_ac": 12,
"gnomad_exomes_af": 0.00000821189,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262857,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Congenital defect of folate absorption|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.107,
"pos": 28402276,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.734,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_080669.6"
}
]
}