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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: 19-12924700-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12924700&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 11,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "FARSA",
"hgnc_id": 3592,
"hgvs_c": "c.1134G>A",
"hgvs_p": "p.Ala378Ala",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -11,
"transcript": "NM_004461.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7,BS2",
"acmg_score": -11,
"allele_count_reference_population": 444,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"chr": "19",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6200000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 508,
"aa_ref": "A",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1811,
"cdna_start": 1149,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1134,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_004461.3",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.1134G>A",
"hgvs_p": "p.Ala378Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000314606.9",
"protein_coding": true,
"protein_id": "NP_004452.1",
"strand": false,
"transcript": "NM_004461.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 508,
"aa_ref": "A",
"aa_start": 378,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1811,
"cdna_start": 1149,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1134,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000314606.9",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.1134G>A",
"hgvs_p": "p.Ala378Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004461.3",
"protein_coding": true,
"protein_id": "ENSP00000320309.3",
"strand": false,
"transcript": "ENST00000314606.9",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 548,
"aa_ref": "A",
"aa_start": 418,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2057,
"cdna_start": 1395,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1254,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000588025.5",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.1254G>A",
"hgvs_p": "p.Ala418Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468051.1",
"strand": false,
"transcript": "ENST00000588025.5",
"transcript_support_level": 5
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 486,
"aa_ref": "A",
"aa_start": 356,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1748,
"cdna_start": 1086,
"cds_end": null,
"cds_length": 1461,
"cds_start": 1068,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000941155.1",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.1068G>A",
"hgvs_p": "p.Ala356Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000611214.1",
"strand": false,
"transcript": "ENST00000941155.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 477,
"aa_ref": "A",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1720,
"cdna_start": 1059,
"cds_end": null,
"cds_length": 1434,
"cds_start": 1041,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000423140.6",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.1041G>A",
"hgvs_p": "p.Ala347Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000396548.2",
"strand": false,
"transcript": "ENST00000423140.6",
"transcript_support_level": 2
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 475,
"aa_ref": "A",
"aa_start": 345,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1915,
"cdna_start": 1050,
"cds_end": null,
"cds_length": 1428,
"cds_start": 1035,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000908769.1",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.1035G>A",
"hgvs_p": "p.Ala345Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578828.1",
"strand": false,
"transcript": "ENST00000908769.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 376,
"aa_ref": "A",
"aa_start": 293,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1135,
"cdna_start": 881,
"cds_end": null,
"cds_length": 1133,
"cds_start": 879,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000593021.1",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.879G>A",
"hgvs_p": "p.Ala293Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467384.1",
"strand": false,
"transcript": "ENST00000593021.1",
"transcript_support_level": 5
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 247,
"aa_ref": "A",
"aa_start": 117,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1024,
"cdna_start": 364,
"cds_end": null,
"cds_length": 744,
"cds_start": 351,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000908771.1",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.351G>A",
"hgvs_p": "p.Ala117Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578830.1",
"strand": false,
"transcript": "ENST00000908771.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 246,
"aa_ref": "A",
"aa_start": 116,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1022,
"cdna_start": 361,
"cds_end": null,
"cds_length": 741,
"cds_start": 348,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000908770.1",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.348G>A",
"hgvs_p": "p.Ala116Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578829.1",
"strand": false,
"transcript": "ENST00000908770.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 158,
"aa_ref": "A",
"aa_start": 130,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 514,
"cdna_start": 391,
"cds_end": null,
"cds_length": 477,
"cds_start": 390,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000587488.5",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "c.390G>A",
"hgvs_p": "p.Ala130Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000468384.1",
"strand": false,
"transcript": "ENST00000587488.5",
"transcript_support_level": 3
},
{
"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": 1707,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000586146.5",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "n.*388G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468068.1",
"strand": false,
"transcript": "ENST00000586146.5",
"transcript_support_level": 5
},
{
"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": 1831,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000588965.5",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "n.1230G>A",
"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": "ENST00000588965.5",
"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": 1707,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000586146.5",
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"hgvs_c": "n.*388G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468068.1",
"strand": false,
"transcript": "ENST00000586146.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs148613387",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0002787761,
"gene_hgnc_id": 3592,
"gene_symbol": "FARSA",
"gnomad_exomes_ac": 397,
"gnomad_exomes_af": 0.000275602,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 47,
"gnomad_genomes_af": 0.000308816,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.121,
"pos": 12924700,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004461.3"
}
]
}