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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: 19-46775681-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=46775681&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 46775681,
"ref": "G",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000542575.6",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.1455C>A",
"hgvs_p": "p.Tyr485*",
"transcript": "NM_005628.3",
"protein_id": "NP_005619.1",
"transcript_support_level": null,
"aa_start": 485,
"aa_end": null,
"aa_length": 541,
"cds_start": 1455,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 2084,
"cdna_end": null,
"cdna_length": 2882,
"mane_select": "ENST00000542575.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.1455C>A",
"hgvs_p": "p.Tyr485*",
"transcript": "ENST00000542575.6",
"protein_id": "ENSP00000444408.1",
"transcript_support_level": 1,
"aa_start": 485,
"aa_end": null,
"aa_length": 541,
"cds_start": 1455,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 2084,
"cdna_end": null,
"cdna_length": 2882,
"mane_select": "NM_005628.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.927C>A",
"hgvs_p": "p.Tyr309*",
"transcript": "ENST00000594991.5",
"protein_id": "ENSP00000469265.1",
"transcript_support_level": 2,
"aa_start": 309,
"aa_end": null,
"aa_length": 365,
"cds_start": 927,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 1235,
"cdna_end": null,
"cdna_length": 2031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.849C>A",
"hgvs_p": "p.Tyr283*",
"transcript": "NM_001145145.2",
"protein_id": "NP_001138617.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 339,
"cds_start": 849,
"cds_end": null,
"cds_length": 1020,
"cdna_start": 1066,
"cdna_end": null,
"cdna_length": 1864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.849C>A",
"hgvs_p": "p.Tyr283*",
"transcript": "ENST00000434726.6",
"protein_id": "ENSP00000406532.1",
"transcript_support_level": 2,
"aa_start": 283,
"aa_end": null,
"aa_length": 339,
"cds_start": 849,
"cds_end": null,
"cds_length": 1020,
"cdna_start": 1076,
"cdna_end": null,
"cdna_length": 1872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.771C>A",
"hgvs_p": "p.Tyr257*",
"transcript": "NM_001145144.2",
"protein_id": "NP_001138616.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 313,
"cds_start": 771,
"cds_end": null,
"cds_length": 942,
"cdna_start": 944,
"cdna_end": null,
"cdna_length": 1742,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.771C>A",
"hgvs_p": "p.Tyr257*",
"transcript": "ENST00000412532.6",
"protein_id": "ENSP00000397924.1",
"transcript_support_level": 2,
"aa_start": 257,
"aa_end": null,
"aa_length": 313,
"cds_start": 771,
"cds_end": null,
"cds_length": 942,
"cdna_start": 993,
"cdna_end": null,
"cdna_length": 1750,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.771C>A",
"hgvs_p": "p.Tyr257*",
"transcript": "ENST00000593713.2",
"protein_id": "ENSP00000468890.2",
"transcript_support_level": 3,
"aa_start": 257,
"aa_end": null,
"aa_length": 313,
"cds_start": 771,
"cds_end": null,
"cds_length": 942,
"cdna_start": 976,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.771C>A",
"hgvs_p": "p.Tyr257*",
"transcript": "ENST00000598022.2",
"protein_id": "ENSP00000471626.2",
"transcript_support_level": 3,
"aa_start": 257,
"aa_end": null,
"aa_length": 313,
"cds_start": 771,
"cds_end": null,
"cds_length": 942,
"cdna_start": 960,
"cdna_end": null,
"cdna_length": 1384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"hgvs_c": "c.771C>A",
"hgvs_p": "p.Tyr257*",
"transcript": "ENST00000713951.1",
"protein_id": "ENSP00000519244.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 313,
"cds_start": 771,
"cds_end": null,
"cds_length": 942,
"cdna_start": 941,
"cdna_end": null,
"cdna_length": 1739,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "FKRP",
"gene_hgnc_id": 17997,
"hgvs_c": "n.248-971G>T",
"hgvs_p": null,
"transcript": "ENST00000600646.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC1A5",
"gene_hgnc_id": 10943,
"dbsnp": "rs1060043",
"frequency_reference_population": 0.000006575314,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657531,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2800000011920929,
"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": 0.28,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": -0.96,
"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",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000542575.6",
"gene_symbol": "SLC1A5",
"hgnc_id": 10943,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1455C>A",
"hgvs_p": "p.Tyr485*"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000600646.5",
"gene_symbol": "FKRP",
"hgnc_id": 17997,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.248-971G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}