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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: 19-46778905-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=46778905&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SLC1A5",
"hgnc_id": 10943,
"hgvs_c": "c.828C>T",
"hgvs_p": "p.Tyr276Tyr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_005628.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_score": -13,
"allele_count_reference_population": 358906,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6399999856948853,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 541,
"aa_ref": "Y",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2882,
"cdna_start": 1457,
"cds_end": null,
"cds_length": 1626,
"cds_start": 828,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_005628.3",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.828C>T",
"hgvs_p": "p.Tyr276Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000542575.6",
"protein_coding": true,
"protein_id": "NP_005619.1",
"strand": false,
"transcript": "NM_005628.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 541,
"aa_ref": "Y",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2882,
"cdna_start": 1457,
"cds_end": null,
"cds_length": 1626,
"cds_start": 828,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000542575.6",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.828C>T",
"hgvs_p": "p.Tyr276Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005628.3",
"protein_coding": true,
"protein_id": "ENSP00000444408.1",
"strand": false,
"transcript": "ENST00000542575.6",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 547,
"aa_ref": "Y",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2923,
"cdna_start": 1480,
"cds_end": null,
"cds_length": 1644,
"cds_start": 828,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000926641.1",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.828C>T",
"hgvs_p": "p.Tyr276Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596700.1",
"strand": false,
"transcript": "ENST00000926641.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 540,
"aa_ref": "Y",
"aa_start": 275,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2600,
"cdna_start": 1178,
"cds_end": null,
"cds_length": 1623,
"cds_start": 825,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000891611.1",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.825C>T",
"hgvs_p": "p.Tyr275Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000561670.1",
"strand": false,
"transcript": "ENST00000891611.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 496,
"aa_ref": "Y",
"aa_start": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2747,
"cdna_start": 1457,
"cds_end": null,
"cds_length": 1491,
"cds_start": 828,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000926642.1",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.828C>T",
"hgvs_p": "p.Tyr276Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596701.1",
"strand": false,
"transcript": "ENST00000926642.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 365,
"aa_ref": "Y",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2031,
"cdna_start": 608,
"cds_end": null,
"cds_length": 1098,
"cds_start": 300,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000594991.5",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.300C>T",
"hgvs_p": "p.Tyr100Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000469265.1",
"strand": false,
"transcript": "ENST00000594991.5",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 339,
"aa_ref": "Y",
"aa_start": 74,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1864,
"cdna_start": 439,
"cds_end": null,
"cds_length": 1020,
"cds_start": 222,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001145145.2",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.222C>T",
"hgvs_p": "p.Tyr74Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001138617.1",
"strand": false,
"transcript": "NM_001145145.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 339,
"aa_ref": "Y",
"aa_start": 74,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1872,
"cdna_start": 449,
"cds_end": null,
"cds_length": 1020,
"cds_start": 222,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000434726.6",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.222C>T",
"hgvs_p": "p.Tyr74Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000406532.1",
"strand": false,
"transcript": "ENST00000434726.6",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 313,
"aa_ref": "Y",
"aa_start": 48,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1742,
"cdna_start": 317,
"cds_end": null,
"cds_length": 942,
"cds_start": 144,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001145144.2",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.144C>T",
"hgvs_p": "p.Tyr48Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001138616.1",
"strand": false,
"transcript": "NM_001145144.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 313,
"aa_ref": "Y",
"aa_start": 48,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1750,
"cdna_start": 366,
"cds_end": null,
"cds_length": 942,
"cds_start": 144,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000412532.6",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.144C>T",
"hgvs_p": "p.Tyr48Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000397924.1",
"strand": false,
"transcript": "ENST00000412532.6",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 313,
"aa_ref": "Y",
"aa_start": 48,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1774,
"cdna_start": 349,
"cds_end": null,
"cds_length": 942,
"cds_start": 144,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000593713.2",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.144C>T",
"hgvs_p": "p.Tyr48Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468890.2",
"strand": false,
"transcript": "ENST00000593713.2",
"transcript_support_level": 3
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 313,
"aa_ref": "Y",
"aa_start": 48,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1384,
"cdna_start": 333,
"cds_end": null,
"cds_length": 942,
"cds_start": 144,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000598022.2",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.144C>T",
"hgvs_p": "p.Tyr48Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000471626.2",
"strand": false,
"transcript": "ENST00000598022.2",
"transcript_support_level": 3
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 313,
"aa_ref": "Y",
"aa_start": 48,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1739,
"cdna_start": 314,
"cds_end": null,
"cds_length": 942,
"cds_start": 144,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000713951.1",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.144C>T",
"hgvs_p": "p.Tyr48Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000519244.1",
"strand": false,
"transcript": "ENST00000713951.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 469,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2661,
"cdna_start": null,
"cds_end": null,
"cds_length": 1410,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000926643.1",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.825-1482C>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596702.1",
"strand": false,
"transcript": "ENST00000926643.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 463,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2648,
"cdna_start": null,
"cds_end": null,
"cds_length": 1392,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000891610.1",
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"hgvs_c": "c.825-1500C>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000561669.1",
"strand": false,
"transcript": "ENST00000891610.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs2070246",
"effect": "synonymous_variant",
"frequency_reference_population": 0.23037216,
"gene_hgnc_id": 10943,
"gene_symbol": "SLC1A5",
"gnomad_exomes_ac": 314753,
"gnomad_exomes_af": 0.2239,
"gnomad_exomes_homalt": 37893,
"gnomad_genomes_ac": 44153,
"gnomad_genomes_af": 0.290163,
"gnomad_genomes_homalt": 7320,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 45213,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.546,
"pos": 46778905,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_005628.3"
}
]
}