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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: 16-1772656-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=1772656&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MRPS34",
"hgnc_id": 16618,
"hgvs_c": "c.322-10G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 14,
"score": 14,
"transcript": "NM_001300900.2",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "EME2",
"hgnc_id": 27289,
"hgvs_c": "c.-572C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 14,
"score": 14,
"transcript": "NM_001257370.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 14,
"allele_count_reference_population": 34,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.79,
"chr": "16",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Combined oxidative phosphorylation deficiency 32,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7900000214576721,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 218,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 998,
"cdna_start": null,
"cds_end": null,
"cds_length": 657,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_023936.2",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "c.322-10G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000397375.7",
"protein_coding": true,
"protein_id": "NP_076425.1",
"strand": false,
"transcript": "NM_023936.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 218,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 998,
"cdna_start": null,
"cds_end": null,
"cds_length": 657,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000397375.7",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "c.322-10G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_023936.2",
"protein_coding": true,
"protein_id": "ENSP00000380531.3",
"strand": false,
"transcript": "ENST00000397375.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 225,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1040,
"cdna_start": null,
"cds_end": null,
"cds_length": 678,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000177742.7",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "c.322-10G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000177742.3",
"strand": false,
"transcript": "ENST00000177742.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 228,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1022,
"cdna_start": null,
"cds_end": null,
"cds_length": 687,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000890485.1",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "c.322-10G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560544.1",
"strand": false,
"transcript": "ENST00000890485.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 225,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1019,
"cdna_start": null,
"cds_end": null,
"cds_length": 678,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001300900.2",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "c.322-10G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001287829.1",
"strand": false,
"transcript": "NM_001300900.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 217,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1009,
"cdna_start": null,
"cds_end": null,
"cds_length": 654,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000939642.1",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "c.298-10G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000609701.1",
"strand": false,
"transcript": "ENST00000939642.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 210,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 955,
"cdna_start": null,
"cds_end": null,
"cds_length": 633,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000890486.1",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "c.298-10G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560545.1",
"strand": false,
"transcript": "ENST00000890486.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 116,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 721,
"cdna_start": null,
"cds_end": null,
"cds_length": 351,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000939641.1",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "c.16-10G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000609700.1",
"strand": false,
"transcript": "ENST00000939641.1",
"transcript_support_level": null
},
{
"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": 713,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000569585.1",
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"hgvs_c": "n.43G>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": "ENST00000569585.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 379,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7022,
"cdna_start": null,
"cds_end": null,
"cds_length": 1140,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001257370.2",
"gene_hgnc_id": 27289,
"gene_symbol": "EME2",
"hgvs_c": "c.-572C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000568449.7",
"protein_coding": true,
"protein_id": "NP_001244299.1",
"strand": true,
"transcript": "NM_001257370.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 379,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7022,
"cdna_start": null,
"cds_end": null,
"cds_length": 1140,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000568449.7",
"gene_hgnc_id": 27289,
"gene_symbol": "EME2",
"hgvs_c": "c.-572C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001257370.2",
"protein_coding": true,
"protein_id": "ENSP00000457353.1",
"strand": true,
"transcript": "ENST00000568449.7",
"transcript_support_level": 1
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.917146664306661,
"dbsnp": "rs563189672",
"effect": "intron_variant",
"frequency_reference_population": 0.000021196558,
"gene_hgnc_id": 16618,
"gene_symbol": "MRPS34",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.00000757758,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 23,
"gnomad_genomes_af": 0.000150934,
"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": "Pathogenic",
"phenotype_combined": "Combined oxidative phosphorylation deficiency 32|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.419,
"pos": 1772656,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9580000042915344,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.93,
"transcript": "NM_001300900.2"
}
]
}