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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: 19-49650959-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49650959&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SCAF1",
"hgnc_id": 30403,
"hgvs_c": "c.570C>T",
"hgvs_p": "p.Pro190Pro",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_021228.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_score": -3,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.014000000432133675,
"computational_source_selected": "REVEL",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1312,
"aa_ref": "P",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4222,
"cdna_start": 610,
"cds_end": null,
"cds_length": 3939,
"cds_start": 570,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_021228.3",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.570C>T",
"hgvs_p": "p.Pro190Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000360565.8",
"protein_coding": true,
"protein_id": "NP_067051.2",
"strand": true,
"transcript": "NM_021228.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1312,
"aa_ref": "P",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4222,
"cdna_start": 610,
"cds_end": null,
"cds_length": 3939,
"cds_start": 570,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000360565.8",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.570C>T",
"hgvs_p": "p.Pro190Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_021228.3",
"protein_coding": true,
"protein_id": "ENSP00000353769.2",
"strand": true,
"transcript": "ENST00000360565.8",
"transcript_support_level": 2
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1319,
"aa_ref": "P",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4206,
"cdna_start": 597,
"cds_end": null,
"cds_length": 3960,
"cds_start": 591,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000892601.1",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.591C>T",
"hgvs_p": "p.Pro197Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000562660.1",
"strand": true,
"transcript": "ENST00000892601.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1312,
"aa_ref": "P",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4233,
"cdna_start": 614,
"cds_end": null,
"cds_length": 3939,
"cds_start": 570,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000892599.1",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.570C>T",
"hgvs_p": "p.Pro190Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000562658.1",
"strand": true,
"transcript": "ENST00000892599.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1311,
"aa_ref": "P",
"aa_start": 189,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4226,
"cdna_start": 607,
"cds_end": null,
"cds_length": 3936,
"cds_start": 567,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000892600.1",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.567C>T",
"hgvs_p": "p.Pro189Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000562659.1",
"strand": true,
"transcript": "ENST00000892600.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 202,
"aa_ref": "P",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 662,
"cdna_start": 623,
"cds_end": null,
"cds_length": 609,
"cds_start": 570,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000598359.5",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.570C>T",
"hgvs_p": "p.Pro190Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000473210.1",
"strand": true,
"transcript": "ENST00000598359.5",
"transcript_support_level": 3
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1315,
"aa_ref": "P",
"aa_start": 193,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4249,
"cdna_start": 637,
"cds_end": null,
"cds_length": 3948,
"cds_start": 579,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011527194.4",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.579C>T",
"hgvs_p": "p.Pro193Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011525496.1",
"strand": true,
"transcript": "XM_011527194.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1312,
"aa_ref": "P",
"aa_start": 190,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4686,
"cdna_start": 1074,
"cds_end": null,
"cds_length": 3939,
"cds_start": 570,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_005259122.6",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.570C>T",
"hgvs_p": "p.Pro190Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005259179.1",
"strand": true,
"transcript": "XM_005259122.6",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1222,
"aa_ref": "P",
"aa_start": 100,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4042,
"cdna_start": 430,
"cds_end": null,
"cds_length": 3669,
"cds_start": 300,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017027083.3",
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"hgvs_c": "c.300C>T",
"hgvs_p": "p.Pro100Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882572.1",
"strand": true,
"transcript": "XM_017027083.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs373203311",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0000014446754,
"gene_hgnc_id": 30403,
"gene_symbol": "SCAF1",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000144468,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.271,
"pos": 49650959,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.014,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_021228.3"
}
]
}