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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: 4-56484837-GCA-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56484837&ref=GCA&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BS2"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "SRP72",
"hgnc_id": 11303,
"hgvs_c": "c.1064_1065delCA",
"hgvs_p": "p.Thr355fs",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_006947.4",
"verdict": "Likely_benign"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000289393",
"hgnc_id": 58796,
"hgvs_c": "n.133-7068_133-7067delTG",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000737350.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_score": -4,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "4",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Autosomal dominant aplasia and myelodysplasia,not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 671,
"aa_ref": "T",
"aa_start": 355,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3855,
"cdna_start": 1083,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1064,
"consequences": [
"frameshift_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_006947.4",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1064_1065delCA",
"hgvs_p": "p.Thr355fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000642900.1",
"protein_coding": true,
"protein_id": "NP_008878.3",
"strand": true,
"transcript": "NM_006947.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 671,
"aa_ref": "T",
"aa_start": 355,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3855,
"cdna_start": 1083,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1064,
"consequences": [
"frameshift_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000642900.1",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1064_1065delCA",
"hgvs_p": "p.Thr355fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006947.4",
"protein_coding": true,
"protein_id": "ENSP00000495128.1",
"strand": true,
"transcript": "ENST00000642900.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 610,
"aa_ref": "T",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2406,
"cdna_start": 900,
"cds_end": null,
"cds_length": 1833,
"cds_start": 881,
"consequences": [
"frameshift_variant"
],
"exon_count": 17,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000510663.6",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.881_882delCA",
"hgvs_p": "p.Thr294fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424576.1",
"strand": true,
"transcript": "ENST00000510663.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 669,
"aa_ref": "T",
"aa_start": 355,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3300,
"cdna_start": 1105,
"cds_end": null,
"cds_length": 2010,
"cds_start": 1064,
"consequences": [
"frameshift_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000925431.1",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1064_1065delCA",
"hgvs_p": "p.Thr355fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595490.1",
"strand": true,
"transcript": "ENST00000925431.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 610,
"aa_ref": "T",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3672,
"cdna_start": 900,
"cds_end": null,
"cds_length": 1833,
"cds_start": 881,
"consequences": [
"frameshift_variant"
],
"exon_count": 17,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001267722.2",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.881_882delCA",
"hgvs_p": "p.Thr294fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001254651.1",
"strand": true,
"transcript": "NM_001267722.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 566,
"aa_ref": "T",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2274,
"cdna_start": 768,
"cds_end": null,
"cds_length": 1701,
"cds_start": 749,
"consequences": [
"frameshift_variant"
],
"exon_count": 16,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000925432.1",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.749_750delCA",
"hgvs_p": "p.Thr250fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595491.1",
"strand": true,
"transcript": "ENST00000925432.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 333,
"aa_ref": "T",
"aa_start": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1006,
"cdna_start": 832,
"cds_end": null,
"cds_length": 1004,
"cds_start": 830,
"consequences": [
"frameshift_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000505314.2",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.830_831delCA",
"hgvs_p": "p.Thr277fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000425190.3",
"strand": true,
"transcript": "ENST00000505314.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 548,
"aa_ref": "T",
"aa_start": 355,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3079,
"cdna_start": 1083,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1064,
"consequences": [
"frameshift_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_024454192.2",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "c.1064_1065delCA",
"hgvs_p": "p.Thr355fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024309960.1",
"strand": true,
"transcript": "XM_024454192.2",
"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": 3969,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NR_151856.2",
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"hgvs_c": "n.1083_1084delCA",
"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": "NR_151856.2",
"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": 1060,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000737350.1",
"gene_hgnc_id": 58796,
"gene_symbol": "ENSG00000289393",
"hgvs_c": "n.133-7068_133-7067delTG",
"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": "ENST00000737350.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs587776907",
"effect": "frameshift_variant",
"frequency_reference_population": 0.0000037197676,
"gene_hgnc_id": 11303,
"gene_symbol": "SRP72",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.0000034227,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657168,
"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": "Uncertain significance",
"phenotype_combined": "Autosomal dominant aplasia and myelodysplasia|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.832,
"pos": 56484837,
"ref": "GCA",
"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_006947.4"
}
]
}