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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: 12-50104089-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=50104089&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 11,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7"
],
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"gene_symbol": "GPD1",
"hgnc_id": 4455,
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -11,
"transcript": "NM_005276.4",
"verdict": "Benign"
},
{
"benign_score": 10,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000295262",
"hgnc_id": null,
"hgvs_c": "n.914+7616G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -10,
"transcript": "ENST00000728910.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7",
"acmg_score": -11,
"allele_count_reference_population": 31,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"chr": "12",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.30000001192092896,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 349,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2887,
"cdna_start": 82,
"cds_end": null,
"cds_length": 1050,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_005276.4",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000301149.8",
"protein_coding": true,
"protein_id": "NP_005267.2",
"strand": true,
"transcript": "NM_005276.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 349,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2887,
"cdna_start": 82,
"cds_end": null,
"cds_length": 1050,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000301149.8",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005276.4",
"protein_coding": true,
"protein_id": "ENSP00000301149.3",
"strand": true,
"transcript": "ENST00000301149.8",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 383,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2982,
"cdna_start": 82,
"cds_end": null,
"cds_length": 1152,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000942603.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612662.1",
"strand": true,
"transcript": "ENST00000942603.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 375,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1733,
"cdna_start": 81,
"cds_end": null,
"cds_length": 1128,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000872078.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542137.1",
"strand": true,
"transcript": "ENST00000872078.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 360,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1689,
"cdna_start": 82,
"cds_end": null,
"cds_length": 1083,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000872076.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542135.1",
"strand": true,
"transcript": "ENST00000872076.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 359,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2920,
"cdna_start": 82,
"cds_end": null,
"cds_length": 1080,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000872073.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542132.1",
"strand": true,
"transcript": "ENST00000872073.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 354,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1671,
"cdna_start": 82,
"cds_end": null,
"cds_length": 1065,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000872077.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542136.1",
"strand": true,
"transcript": "ENST00000872077.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 348,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2899,
"cdna_start": 104,
"cds_end": null,
"cds_length": 1047,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000942601.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612660.1",
"strand": true,
"transcript": "ENST00000942601.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 345,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2875,
"cdna_start": 82,
"cds_end": null,
"cds_length": 1038,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000872074.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542133.1",
"strand": true,
"transcript": "ENST00000872074.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 344,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1640,
"cdna_start": 81,
"cds_end": null,
"cds_length": 1035,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000942604.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612663.1",
"strand": true,
"transcript": "ENST00000942604.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 326,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2818,
"cdna_start": 82,
"cds_end": null,
"cds_length": 981,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001257199.2",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001244128.1",
"strand": true,
"transcript": "NM_001257199.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 326,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1591,
"cdna_start": 82,
"cds_end": null,
"cds_length": 981,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000548814.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000446768.1",
"strand": true,
"transcript": "ENST00000548814.1",
"transcript_support_level": 2
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 302,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1515,
"cdna_start": 82,
"cds_end": null,
"cds_length": 909,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000872075.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542134.1",
"strand": true,
"transcript": "ENST00000872075.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 270,
"aa_ref": "N",
"aa_start": 13,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2659,
"cdna_start": 94,
"cds_end": null,
"cds_length": 813,
"cds_start": 39,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000942602.1",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "c.39C>T",
"hgvs_p": "p.Asn13Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612661.1",
"strand": true,
"transcript": "ENST00000942602.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 740,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000547190.5",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "n.82C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000547190.5",
"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": 573,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000547964.5",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "n.39C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000448244.1",
"strand": true,
"transcript": "ENST00000547964.5",
"transcript_support_level": 4
},
{
"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": 757,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000551939.5",
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"hgvs_c": "n.82C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000551939.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 946,
"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": "ENST00000728910.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000295262",
"hgvs_c": "n.914+7616G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000728910.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.801002941273348,
"dbsnp": "rs922947825",
"effect": "splice_region_variant,synonymous_variant",
"frequency_reference_population": 0.000019207748,
"gene_hgnc_id": 4455,
"gene_symbol": "GPD1",
"gnomad_exomes_ac": 30,
"gnomad_exomes_af": 0.0000205231,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657194,
"gnomad_genomes_homalt": 0,
"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": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.786,
"pos": 50104089,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.36399999260902405,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005276.4"
}
]
}