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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: 17-6687643-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=6687643&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SLC13A5",
"hgnc_id": 23089,
"hgvs_c": "c.1461G>T",
"hgvs_p": "p.Pro487Pro",
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": -5,
"transcript": "NM_177550.5",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "C17orf100",
"hgnc_id": 34494,
"hgvs_c": "n.*325-5222C>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -4,
"transcript": "ENST00000635042.1",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000290366",
"hgnc_id": null,
"hgvs_c": "n.511-2233C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -4,
"transcript": "ENST00000634558.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_score": -5,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.56,
"chr": "17",
"clinvar_classification": "Likely benign",
"clinvar_disease": " 25,Developmental and epileptic encephalopathy",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5600000023841858,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 568,
"aa_ref": "P",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3231,
"cdna_start": 1497,
"cds_end": null,
"cds_length": 1707,
"cds_start": 1461,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_177550.5",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1461G>T",
"hgvs_p": "p.Pro487Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000433363.7",
"protein_coding": true,
"protein_id": "NP_808218.1",
"strand": false,
"transcript": "NM_177550.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 568,
"aa_ref": "P",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3231,
"cdna_start": 1497,
"cds_end": null,
"cds_length": 1707,
"cds_start": 1461,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000433363.7",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1461G>T",
"hgvs_p": "p.Pro487Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_177550.5",
"protein_coding": true,
"protein_id": "ENSP00000406220.2",
"strand": false,
"transcript": "ENST00000433363.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 522,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1723,
"cdna_start": null,
"cds_end": null,
"cds_length": 1569,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000573648.5",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1438-1305G>T",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000459372.1",
"strand": false,
"transcript": "ENST00000573648.5",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 564,
"aa_ref": "P",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3220,
"cdna_start": 1494,
"cds_end": null,
"cds_length": 1695,
"cds_start": 1461,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000898130.1",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1461G>T",
"hgvs_p": "p.Pro487Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568189.1",
"strand": false,
"transcript": "ENST00000898130.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 551,
"aa_ref": "P",
"aa_start": 470,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3180,
"cdna_start": 1446,
"cds_end": null,
"cds_length": 1656,
"cds_start": 1410,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001284509.2",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1410G>T",
"hgvs_p": "p.Pro470Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001271438.1",
"strand": false,
"transcript": "NM_001284509.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 551,
"aa_ref": "P",
"aa_start": 470,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3176,
"cdna_start": 1446,
"cds_end": null,
"cds_length": 1656,
"cds_start": 1410,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000293800.10",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1410G>T",
"hgvs_p": "p.Pro470Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000293800.6",
"strand": false,
"transcript": "ENST00000293800.10",
"transcript_support_level": 2
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 527,
"aa_ref": "P",
"aa_start": 446,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3098,
"cdna_start": 1371,
"cds_end": null,
"cds_length": 1584,
"cds_start": 1338,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000949501.1",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1338G>T",
"hgvs_p": "p.Pro446Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619560.1",
"strand": false,
"transcript": "ENST00000949501.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 525,
"aa_ref": "P",
"aa_start": 444,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3102,
"cdna_start": 1368,
"cds_end": null,
"cds_length": 1578,
"cds_start": 1332,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001284510.2",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1332G>T",
"hgvs_p": "p.Pro444Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001271439.1",
"strand": false,
"transcript": "NM_001284510.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 525,
"aa_ref": "P",
"aa_start": 444,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1738,
"cdna_start": 1365,
"cds_end": null,
"cds_length": 1578,
"cds_start": 1332,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000381074.8",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1332G>T",
"hgvs_p": "p.Pro444Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000370464.4",
"strand": false,
"transcript": "ENST00000381074.8",
"transcript_support_level": 2
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 496,
"aa_ref": "P",
"aa_start": 415,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3009,
"cdna_start": 1278,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1245,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000898131.1",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1245G>T",
"hgvs_p": "p.Pro415Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568190.1",
"strand": false,
"transcript": "ENST00000898131.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 93,
"aa_ref": "P",
"aa_start": 43,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 419,
"cdna_start": 130,
"cds_end": null,
"cds_length": 282,
"cds_start": 129,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000570687.1",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.129G>T",
"hgvs_p": "p.Pro43Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000460037.1",
"strand": false,
"transcript": "ENST00000570687.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 498,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1957,
"cdna_start": null,
"cds_end": null,
"cds_length": 1497,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_011523795.4",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.*134G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011522097.1",
"strand": false,
"transcript": "XM_011523795.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 522,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3093,
"cdna_start": null,
"cds_end": null,
"cds_length": 1569,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001143838.3",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1438-1305G>T",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001137310.1",
"strand": false,
"transcript": "NM_001143838.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 468,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2925,
"cdna_start": null,
"cds_end": null,
"cds_length": 1407,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000898132.1",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "c.1276-1305G>T",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568191.1",
"strand": false,
"transcript": "ENST00000898132.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 5398,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000574580.2",
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"hgvs_c": "n.2478G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000574580.2",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1009,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000634558.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000290366",
"hgvs_c": "n.511-2233C>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000634558.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 977,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000634823.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000290366",
"hgvs_c": "n.265-5222C>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000634823.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1062,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000635042.1",
"gene_hgnc_id": 34494,
"gene_symbol": "C17orf100",
"hgvs_c": "n.*325-5222C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491523.1",
"strand": true,
"transcript": "ENST00000635042.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs374067396",
"effect": "synonymous_variant",
"frequency_reference_population": 6.8756026e-7,
"gene_hgnc_id": 23089,
"gene_symbol": "SLC13A5",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.8756e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "Developmental and epileptic encephalopathy, 25",
"phylop100way_prediction": "Benign",
"phylop100way_score": -4.232,
"pos": 6687643,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.17000000178813934,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.17,
"transcript": "NM_177550.5"
}
]
}